Population structure dynamics of Taiwan rice accessions over thousands of years as revealed by archaeological, morphological and genome sequencing information

Population structure dynamics of Taiwan rice accessions over thousands of years as revealed by archaeological, morphological and genome sequencing information | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Population structure dynamics of Taiwan rice accessions over thousands of years as revealed by archaeological, morphological and genome sequencing information Cheng-chieh Wu, Chun-Kai Liu, Yuan-Ching Tsai, Fu-Jin Wei, Lin-Tzu Huang, and 19 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3218983/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Background Cultivation of rice ( Oryza sativa ) started in Taiwan about 5000 years ago. Here we studied changes in the rice population during this period by using archaeological, morphological, genetic and genomic strategies. We studied the grain size changes of carbonized rice from excavated sites. We also revealed the variations in landraces collected from the indigenous villages and landraces that arrived in Taiwan from southern China about 400 years ago. Some modern varieties were also used in the current study. Results The very early cultivated rice must have been temperate japonica type, and the seeds were relatively small. Rice seeds became relatively bigger around 1500 BP, with some indica or tropical japonica ones. Most, if not all, of the i ndica rice were not primitive types, suggesting they arrived in Taiwan rather late. Together, temperate, subtropical, tropical japonica and indica rice have been cultivated by indigenous people for a long period, with all in upland practice. However, only indica landraces were cultivated in the plain region from the early 17th century to about 100 years ago, when japonica rice accessions become dominant. We illustrated huge differences in genetic diversity among the subpopulations of Taiwan rice accessions, and many of these lines showed stress resistance to drought, flooding and ABA treatments. Conclusion We show how civilization, human migration, taste preference, natural introgression and breeding programs have shaped the population structure of Taiwan rice accessions over thousands of years. We also indicate that Taiwanese indigenous peoples and traditional farmers have kept the rice landraces for hundreds and up to thousands of years. With many old traits preserved, they are good resources for future breeding programs. Excavated rice grain genetic diversity population structure stress tolerance Figures Figure 1 Figure 2 Introduction Asian cultivated rice ( Oryza sativa ) is one of the most important crops in the world and the most widely consumed. The rice was genetically divided into 2 main subspecies, japonica and indica , with distinct morphological and physiological characteristics (reviewed by atsuo and Hoshikawa, 1993). Later on, with the analysis of molecular markers nd whole genome sequencing (3KRGP 2014), rice was found to contain 5 major subpopulations: aus , indica , temperate japonica , tropical japonica , and aromatic . In 2018, a detailed analysis of the 3K accessions further classified indica rice into ind 1a, ind 1b, ind 2 and ind 3 and japonica rice into tropical, subtropical and temperate japonica (Wang et al. 2018). According to archaeological studies, the early domesticated (i.e., non-shattering) cultivated rice in China was the japonica type, about 8,000 years ago, collected from Baligang in the Yellow River-Huai River-Plain (Deng et al. 2015). Although there was rice collected from the Shangshan site about 9,000 years ago in the Lower Yangtze region (Liu et al. 2007; Zuo et al. 2017), most of them are still shattering. Wild rice ancestral to indica was present in the northern Indian subcontinent before the arrival of non-shattering japonica (Silva et al. 2018). Indica rice was domesticated after the arrival of domesticated japonica rice, about 4,000 years ago, in the Ganges plains of eastern India (Fuller et al. 2010). PCR amplification followed by sequencing of fragmented products using nuclear- and plastic- primers of hundreds of archaeological grains excavated from India (2 archaeological sites) and Thailand (4 sites) dated 2500 to 1500 before present (BP) revealed that the rice was predominantly japonica in Thailand and a mixture of japonica and indica with indica in the minority in India (Castillo et al. 2016). Thus, the movement of indica rice accessions to Southeast Asia (SEA) and East Asia (EA) was relatively late as compared with japonica rice cultivation. According to the archaeological studies, there are thousands of carbonized rice grains found in Nan-kuan-li (NKL) and Nan-kuan-li East (NKLE) excavated sites in southern Taiwan. Ten 14 C dates obtained from these sites indicate that they were there between 5,000 to 4,500 BP. Other crop remains such as foxtail millet ( Setaria italica ) and broomcorn millet ( Panicum miliaceum ) as well as farming tools such as shell knives and stone hoes were discovered (Hsieh et al. 2011; Tsang et al. 2017). Thus, rice and millet farming may have been an important food source for people living about 5000 years ago in southern Taiwan. Taiwan indigenous people are the original inhabitants of Taiwan. Their ancestors may have been living in Taiwan for thousands of years before the Han Chinese immigration began in the 17th century. Taiwanese aborigines are Austronesian-speaking peoples and were demonstrated as the origin of Austronesian languages located in the Philippines, Indonesia, Malaysia, Madagascar, Polynesia and Oceania (see e.g., Hill et al 2007). The dispersal is presumed to have led to the spread of Austronesian languages, cultural similarities, and agriculture and so on (Blust 1995; Bellwood 1997; Bellimod 2004; Bellwood 2023). Thus, the Taiwanese indigenous people have played important roles as the bridge of the mainland and the Pacific, and the analyses of early agriculture are critical. According to this “Out-of-Taiwan” hypothesis, rice, millet and taro are the three among many others important for the dispersal. The linguistic studies also coincide well with the flow as most people, if not all, in this area called rice *pajay before Columbus’ time (Sagart 2011). The population structure of domesticated rice species has been influenced by civilization, human migration, taste preference, plant introgression, etc., during the history of the cultivation. Since the 20th century, plant breeding programs have played critical roles in crop production; thus hybridization between parental cultivars with desirable traits followed by intensive artificial selection are important for the development of new varieties. In the current study, we used carbonized rice grains from several excavated sites in Taiwan to reveal the seed size changes across thousands of years on the island. We also used whole genome sequencing to reveal the population structure differences among the current Taiwan rice accessions with the view that 1) the early rice accessions in Taiwan had been cultivated for thousands of years, 2) rice cultivation changed with the arrival of the Han people about 400 years ago, 3) changes from indica to japonica rice during the Japanese colonial period started about 100 years ago, and 4) the modern breeding period has existed since the early 20th century. The questions we asked included 1) Which type was the early rice that arrived in Taiwan in ancient times, 2) What are the reasons for changes in major rice populations, 3) What are the relationships in rice populations with the nearby regions, and 4) How did the domestication/adaptation alleles change in different populations. We show how civilization, human migration, taste preference, natural introgression and breeding programs have shaped the population structure of Taiwan rice accessions over thousands of years. Materials and Methods Archaeological materials Hundreds of carbonized rice grains were collected from 4 excavated sites belonging to 4 cultures by using the floating method. The sites are NKLE (23º6'58"N, 120º16'35"E, altitude 0.5 m, 4800 BP) of the Dapenkeng culture (4800 − 3300 BP), Youhsienfang (YHF, 23°06'54.0"N 120°16'25.0"E, altitude 6 m) of the Niuchouzi culture (3800 − 3300 BP), Wuchiantsuo (WCT, 23°05'39.0"N 120°16'25.0"E, altitude 7 m) of the Niaosong culture (1400 − 500 BP), and Huilaili (HLL, 24º09'42.8"N, 120º38'11.6"E, altitude 73 m, 1300 BP) of the Fanziyuen culture (2000-400BP). In total, 100 carbonized rice samples from each site were used to estimate seed width, length and thickness by using a digital ruler (Mitutoyo Co., Japan) with accuracy of 0.01 mm. The Chinese translation of the excavated sites and cultures are listed in Table S1 . Plant materials and growth condition The seeds of the indigenous rice accessions, landraces and modern varieties were obtained from the National Plant Genetic Resources Center (NPGRC), Taiwan Agricultural Research Institute (TARI), Taiwan. The seeds were collected from the indigenous peoples of the mountain regions of different tribes. Part of the samples were collected around 1900 and the rest in recent years. The accession names for all seeds are in Table S2 . The plants of single seed descent were cultivated until tillering stage in an Academia Sinica greenhouse under natural light. Healthy leaves without insect damage from one single plant were harvested, frozen under liquid nitrogen and stored at -80℃ for DNA extraction. Whole genome sequencing and single nucleotide polymorphism (SNP) calling Genomic DNA was extracted from leaves by using a DNeasy Plant Mini Kit (Qiagen) following the manufacturer’s protocol. DNA was prepared for Illumina genome sequencing using the Illumina Hiseq2000 instrument with a 2 x 150-bp read configuration. A few of the Taiwan rice accessions were sequenced in the 3K rice project (3KRGP 2014). Sequencing data for these accessions are available from the NCBI Short Read Archive (Bioproject accession nos. PRJNA485658, PRJNA373799, PRJNA623980, and PRJEB6180). The paired reads were mapped against the Os-Nipponbare-Reference-IRGSP-1.0 database (IRGSP 2005; Kawahara et al. 2013). SAMtools (Li et al. 2009) and VCFtools (Danecek et al. 2011) were used to handle the sequence alignment/map format (SAM) and variant call format (VCF) of the file. To detect SNPs and small indels, we used the command lines in the section “Variant Calling” in “Workflows” of the SAMtools manual. The information on SNPs and small indels was recorded in VCF files. The detailed methods were similar to those described previously (Wei et al. 2016a; Wu et al. 2020a). Scoring of grain-related traits Several grain-related traits were screened: long awn, red caryopsis, glutinous, seed width and seed length. Awns > 2 cm were defined as long awns. Ground rice grain was treated with 0.2% iodine reagent and scored 5 min later for the glutinous (sticky) phenotype. Estimation of diversity of domestication- or adaptation-related genes Twenty domestication- or adaptation-related genes were used to evaluate the gene diversity. They are An1 (Luo et al. 2013), An2 (Gu et al. 2015; Hua et al. 2015), Bh4 (Zhu et al. 2011), Cold1 (Ma et al. 2015), Ehd1 (Doi et al. 2004), Gn1 (Ashikari et al. 2005), Hd3a (Tamaki et al. 2007), IPA1 (Lu et al. 2013), Lg1 (Zhu et al. 2013), OsLg1 (Ishii et al. 2013), OsC1 (Saitoh et al. 2004), Phr1 (Yu et al. 2008), Prog1 (Jin et al. 2008), qSH1 (Konishi et al. 2006), qSW5 (Shomura et al. 2008), RAE2 (Bessho-Uehara et al. 2016), Rc (Sweeney et al. 2006), TGW6 (Ishimaru et al. 2013), TT1 (Li et al. 2015) and Waxy (Wang et al. 1995). These genes are related to plant stature, grain phenotypes, temperature tolerance or photoperiod sensitivity. Detailed information for these genes is in Table S3 . Genomic sequences were aligned by using MUSCLE (Edgar 2004a, b). The − 1 Mb to + 1 Mb region of each of these genes was used for the analysis. Statistical analysis involved using DNAsp.v6 (Rozas et al. 2017). Items analyzed included number of polymorphic (segregating) sites (S), total number of mutations (Eta), average number of nucleotide differences ( k ), nucleotide diversity ( π ) (Tajima 1983), theta (per sequence) from Eta θ , and Watterson’s estimator of theta (per site) from Eta θw (Watterson 1975). The neutrality test, with Tajima's D value, was used to test the neutral mutation hypothesis (Tajima 1989). The D value was based on the discrepancy between π and θw ; thus, negative values indicate excess low-frequency polymorphism. Results Continuous rice cultivation in Taiwan from 5000 years ago The earliest Taiwan carbonized rice grains were found in the excavated sites about 5000 years ago. Thousands of carbonized rice grains were found in NKL and NKLE in southern Taiwan from 5000 − 4500 BP (Hsieh et al. 2011; Zang and Li 2015). Rice was found continuously in the southern part in YHF (3800 − 3300 BP, Zang and Li 2015), WCT (1800 − 500 BP, Zang and Li 2015) and Siliao (2300 − 600 BP, Liu 2011. There were also reports of early rice in Fushan (4500 − 3500 BP) and Chaolaiqiao (4500 − 3500 BP) during the middle Neolithic period in eastern Taiwan (Wu et al. 2016; Deng et al. 2022). In central Taiwan, early rice was found in Anhe (4800 − 4000 BP, Deng et al. 2022) and HLL (1300 BP, Chu 2016). In northern Taiwan, carbonized rice grains were found in the Zhiwuyuan site (Taipei Botanical Garden) (4500 BP, Deng et al . 2022) and Chishanyan site (4000 − 3000 BP, Huang 1984). Thus, archaeological studies indicated continuous rice cultivations in Taiwan from about 5000 years ago to the present. Using 100 carbonized seeds from 4 excavated sites, we studied the seed size changes by measuring the seed length, width and thickness. Figure 1 shows that early rice seeds were relatively small: with length 3 to 4.5 mm, width 1.8 to 2.9 mm and thickness 1.1 to 2 mm at NKLE and YHF, both located in southern Taiwan and before 3300 BP. The seed size variations during this period were rather small. For the seeds with a wide range of time (~ 1400 − 500 BP) in the south (i.e., WCT), the length varied from 4.5 to 7 mm, width 2.2 to 3.6 mm and thickness 1.3 to 2.9 mm. Thus, the seed size was significantly larger than earlier ones and with large variation. Some of these seeds were double in size as compared with the two earlier ones. About the same time (1300 BP) in central Taiwan (i.e., HLL), seed length was 3.8 to 6 mm, width 1.8 to 3 mm, and thickness 1.2 to 2.1 mm. The seeds were larger than seeds from NKLE and YHF and smaller than those from WCT, again with large variation. Therefore, rice seed size in Taiwan has changed over thousands of years, from relatively small and round to large with an oblonga shape. Total of 265 accessions were used in the current genomic study A total of 265 rice accessions collected in Taiwan were used in the study (Table 1 , Table S2 ). These included 129 accessions collected from indigenous villages, 58 belonging to those brought to Taiwan about 400 years ago, 17 breeding lines, 58 modern varieties and one weedy rice. In addition to these 263 lines, 2 wild rice accessions were collected in Ba-der, Taoyuan. All of the 263 + 2 accessions (listed in Table S2 ) underwent whole genome sequencing followed by further analysis. Table 1 The subgroups of Taiwanese rice accessions used int the study. No aus or aromatic types were found in local lines. Temperate japonica Subtropical japopnica Tropical japonica indica Admixture Total Indigenous 58 17 12 39 3 129 Mingching 0 0 0 58 0 58 Modern 54 0 4 16 1 75 Red rice (weedy) 0 0 0 1 0 1 total 112 17 16 114 4 263 Sum: 263 + 2 wild relatives Many rice landraces had been cultivated by indigenous peoples in the mountainous regions with an upland practice. A total of 60 upland rice accessions were collected from the indigenous villages from 1895 to the early 1900s. These accessions were since propagated (renewed) about every 10 years by rice breeders, and seeds were stored in NPGRC, TARI. There are only names for this seed resource, without other information such as collecting time, villages and tribes. Some rice breeders visited mountain regions and collected more accessions in recent years and added another approximately 70 lines, with information on tribes collected. These accessions are highly diverse in seed morphology, plant height, plant stature, heading behavior, etc., as shown in our previous studies (Hsieh et al. 2011; Sagart et al. 2018; Wu et al. 2020a). The Han people migrated to Taiwan from the southeast coastal area in China, mainly Fujian and Guangdong, to Taiwan during the late Ming to early Ching Dynasty about 400 years ago. The rice accessions they brought were designated “Ming-Ching” in the current study. According to the literature, there were 1,679 Ming-Ching accessions during the survey in 1906, and the breeders reduced these to 547 lines after screening and elimination according to similarity in morphology (Iso 1944). All these resources were also stored in NPGRC. We chose 58 accessions from this collection for the current analysis. These accessions represented the old landraces in southern China about 400 years ago. Modern breeding programs have been applied for improving rice varieties, including japonica and indica , in Taiwan since the 1920s. Both breeding lines (the intermediate lines during the breeding process for new varieties) and modern varieties (finished the complete breeding process and were assigned names) were chosen for this study; they belong to the category “modern” rice. Red rice, also known as weedy rice, has been a problem in rice production practice in Taiwan in recent years (Huang et al. 2021; Wu et al. 2020b). One red rice accession was also used for the present analysis. A wild rice ( Oryza rufipogon ) population existed in northern Taiwan previously and had become extinct on the site around 1978 (Kiang 1979). Some of these accessions were kept by rice breeders in the Miaoli Agriculture Research Station, and we received 2 lines for the current study. Classification of the indigenous upland rice accessions We prepared a rice genomics and phenomics resource of 500 accessions primarily with Taiwan rice accessions previously described (Wu et al. 2022). This resource consists of the genome sequencing data for 265 Taiwan accessions along with temperate japonica , subtropical japonica , tropical japonica , indica , aus , and aromatic accessions collected from other Asia countries where rice is the major staple food. We used 500 accessions for phylogenetic, structure and genome-wide association analyses. Structure analysis at K = 9 (Fig. 2 , Wu et al. 2022) could separate the accessions into 9 categories: japonica accessions into 4 groups (i.e., V1, V2, V4 and V7), indica into 4 groups (V3, V5, V6 and V8) and wild rice accessions as V9. The 265 lines in the current study were classified into these 9 groups (Table 2 ), with the detailed information for each accession presented in Table S2 . Table 2 Detail information of the V1 to V9 groups classified by using structure analysis. Group # Subtype Total number Taiwan number* Descriptions V1 Temp jap 40 40 (40) All accessions were from Taiwan, with primitive traits such as long awn and shattered. V2 Subtrop jap 35 17 (17) Most were from Indochina. V3 Indica 48 4 (1) Most were from Indian Subcontinent. V4 Temp jap 87 73 (18) Most were modern varieties from Taiwan and Japan V5 Indica 99 9 (2) Most were from Indochina and insular southeast Asia. V6 Indica 55 44 (5) Most were from indigenous and Mingching of Taiwan V7 Trop jap 72 16 (12) Most were from insular southeast Asia. V8 Indica 65 61 (34) Most were from indigenous and Mingching of Taiwan V9 Wild rice 14 1 Wild rice collected in Asia *Accessions numbers collected from Taiwan, with the indigenous ones in brackets. To summarize: the indigenous temperate japonica accessions were grouped into V1 and V4, with the primitive types in V1 and modern ones in V4. For the follow-up analysis, V1 and V4 were assayed differently. Indigenous rice accessions in V2 were subtropical japonica and in V7 tropical japonica . For the indica rice, those in V3 were classified with accessions from the Indian subcontinent and V5 with accessions from the mainland- and insular-SEA. It is intriguing to note that those in V6 and V8 were grouped with Taiwan landraces themselves. We used several early primitive traits such as long awn and red caryopsis to postulate which subtype of rice arrived Taiwan at an early time, that is, indigenous accessions. Table 3 lists the accessions numbers and percentage of these traits. In the indigenous temperate japonica , 4- or 5-fold more accessions have long awns and red caryopsis in V1 versus V4. About half of the indigenous subtropical japonica accessions contained long awns, with none in the tropical japonica lines. In all, 5.9% and 16.7% of the subtropical and tropical japonica accessions had a red caryopsis. Because indica rice arrived from EA and SEA relatively late (Castillo et al. 2016), the early cultivated rice in Taiwan must be the japonica type. From the phenotype of indigenous rice lines, the temperate lines may have arrived the earliest, followed by the subtropical and then tropical lines. However, indica indeed arrived quite late because only 5.1% had long awns. About half (46.2%) of the indigenous indica rice accessions had a red caryopsis, probably because the early indica in nearby regions was still colored rice during that time. Table 3 Phenotyping information of grain-related traits in Taiwan indigenous rice accessions. Long awn Red caryopsis Glutenous endosperm Indigenous Temperate jap (V1) 23/40 = 57.5% 19/40 = 47.5% 36/40 = 90% Temperate jap (V4) 2/18 = 11.1% 2/18 = 11.1% 3/18 = 16.7% Subtropical jap (V2) 9/17 = 52.9% 1/17 = 5.9% 5/17 = 29.4% Tropical jap (V7) 0/12 2/12 = 16.7% 5/12 = 41.7% Indica (V3 + V5 + V6 + V8) 2/39 = 5.1% 18/39 = 46.2% 13/39 = 33.3% Admixture 0/3 1/3 = 33% 0/3 Mingching Indica (V3 + V5 + V6 + V8) 0/58 6/58 = 10.3% 4/58 = 6.9% Modern Admixture 0/1 0/1 0/1 Tropical jap (V7) 0/4 0/4 0/4 Temperate jap (V4) 0/54 0/54 3/54 = 5.6% Indica 0/16 0/16 5/16 = 31% Red rice (weedy) Indica (V6) 0/1 1/1 0/1 Glutinous rice has been important in indigenous villages because it is used to make wine and rice pudding. The wine is important for sacrifice ceremonies as well as at entertainment parties. Thus, we checked the sticky grains: 90%, 16.7%, 29.4%, 41.7% and 33.3% accessions are the glutinous type for temperate V1, temperate V4, subtropical V2, tropical V7 japonica and indica rice, respectively. For comparison, Ming-Ching and modern rice each have much less sticky rice (about or < 10%). Thus, glutinous rice is specifically popular in the indigenous accessions. Only indica landraces were cultivated in the plain region since the Han people arrived in the early 17th century The Han people had been living in the plain region since their arrival and most indigenous villages were moved to high mountain regions. All rice accessions grown in the plain region since then were indica rice according to the history book related to Taiwan rice cultivation (DAFTPG 1989; Teng 2003) and sequencing information (Wu et al. 2022), so most, if not all, landraces cultivated in southern China must have been indica rice during the late Ming Dynasty. In a survey of rice accessions preserved by TARI (searchable at the NPGRC website, https://www.npgrc.tari.gov.tw/npgrc1/index_e.html ), 54 of 450 of these Ming-Ching lines are glutinous and all others are wild type. In addition, 19 of the 450 lines have a red caryopsis and all others are white, and 2 of these lines have long awns. As compared with the indigenous rice accessions, no or only a small proportion of the rice grains of these lines have long awns or red caryopsis. One of the most important traits for the Ming-Ching accessions was semidwarf (sd). This trait was used in the breeding of IR8, the miracle rice, and played important roles in indica rice breeding worldwide since the 1960s (Khush 1995, 1999). This trait came from the Dee-Geo-Woo-Gen (DGWG) sd1 allele, one of the Ming-Ching accessions. The mutation was caused by a 383-bp deletion in the gene GA 20 oxidase-2 (Os01t0883800) (Sasaki et al. 2002), which led to the abolishment of this GA 20 oxidase function. We checked all Ming-Ching accessions and found that in addition to DGWG, another 4 accessions also contained the sd1-DGWG allele: Hsinchu-Ai-Chueh-Chien, Ti-Chueh-Wu-Ko, Ai-Tzu-Chung, and Liu-Tou-Tzu. Major modern rice accessions were japonica rice due to the taste preference during Japanese colonial times During the Japanese colonial period (1895 to 1945), Taiwan rice cultivation had gradually shifted to temperate japonica accessions. According to several reviews, including DAFTPG (1989) and Teng (2003), this huge change was due to the taste preference of Japanese people. All the cultivated accessions in the plain region before 1920 were indica type and there were few japonica types since 1925, with the percentage of indica and japonica being 87.5% and 12.5%, respectively. The earliest japonica variety was Taichung 65, which was designated in 1929 (Iso 1944; Wei et al. 2016b). The percentage of indica type then gradually decreased to 32.9% in 1944. There was a small increase during 1945 and 1946, with the ratio being 47.1% and 65.4%, respectively. The indica rice proportion then gradually decreased again (Teng 2003) and has been less than 10% in the recent decade (data from the Council of Agriculture, Taiwan). By using the sequencing information for new accessions since breeding was applied to rice cultivation, only 4 and 12 breeding lines and new varieties, respectively, for indica rice, versus 13 and 46, respectively, for japonica rice (Table S2 ). Thus, japonica varieties gained more attention in the breeding programs. The sd1 trait has been used in more than 90% of the modern rice varieties worldwide. This DGWG 383-bp deletion was present in all Taiwan modern indica varieties as well as the weedy rice tested. We also checked its presence in the modern japonica varieties. Taikeng 9 had an indica type (IR5470) as one of its parental lines; however, sequence analysis revealed that it did not contain this mutation in the SD1 locus. The same is true for all other japonica varieties without indica rice in their pedigree. Thus, even though the DGWG sd1 allele has been used in most indica and some japonica varieties worldwide, it was not present in any modern Taiwanese japonica variety. Changes in phenotypes related to stress tolerance Previously, we established a resource for rice genome-wide association study with about 500 accessions of selected upland rice and landraces from Taiwan and Asia, along with some modern varieties (Wu et al. 2022). We performed phenotyping studies of seedlings including study of resistance to flooding, drought and abscisic acid (ABA) treatments. Together, information for 19 phenotypes was obtained, including 1) drought survival rate after 25% PEG treatment (severe osmotic stress), 2) ratio of shoot length after flooding treatment for 7 days (compared with control), 3) ratio of root length after flooding treatment for 7 days (compared with control), 4) ratio of total root length after 0.5 µM ABA treatment (compared with control), 5) ratio of crown root length after 0.5 µM ABA treatment (compared with control), 6) ratio of primary root length after 0.5 µM ABA treatment (compared with control), 7) ratio of crown root number after 0.5 µM ABA treatment (compared with control), 8) root length under the control condition, 9) root length after 7 day flooding treatment, 10) shoot length under the control condition, 11) shoot length after 7 day flooding treatment, 12) total root length under the control condition, 13) total root length after 0.5 µM ABA treatment, 14) crown root length under the control condition, 15) crown root length after 0.5 µM ABA treatment, 16) primary root length under the control condition, 17) primary root length after 0.5 µM ABA treatment, 18) crown root number under the control condition, and 19) crown root number after 0.5 µM ABA treatment. Figure 2 illustrates the phenotype histograms for the japonica and indica populations under stress conditions. Panels A and B show the root length response to 7-day flooding treatment, and C and D show the survival rate after 3-day 25% PEG treatment. The red arrows indicate the position of control varieties Tainung 67 ( japonica ) or Taichung Native 1 ( indica ). Two kinds of landraces were included: Ming-Ching and indigenous ones. The results of both modern varieties or landraces was normal distribution for most phenotypes checked. For the drought-resistant trait of indica rice accessions, the distribution was skewed toward more resistance. Even though some landraces showed higher resistance to the stress treatments, some modern varieties also provided similar protection. Supplementary Fig. 1 panels A to AL illustrate the other histograms for the 19 phenotypes. All show a similar trend, that is, normal distribution; some landraces and a few modern varieties feature resistant phenotypes. Changes in genetic diversity We used phylogenetic, structure and principle component analyses to show the diversity and classification of the 500 accessions (Wu et al. 2022). The Taiwanese accessions were grouped into 9 sessions with K = 9 for the structure analysis, as shown in the classification section. We explored the genetic diversity among these groups by checking for the existence of positive selection of 20 domestication- or adaptation-related genes (listed in Table S3 with gene locus information and references). We calculated selection parameters, including π (Tajima 1983), θw (Watterson 1975), as well as Tajima’s D (Tajima 1989), to test the neutral mutation hypothesis. The nearby region (± 1 Mb) of each gene were used for the calculation and the results are listed in Table 4 and Table S4 . The genes of a specific group with significant selection are listed and the information illustrated huge differences among each group. For instance, 19 genes were under selection for Taiwanese V4 group, so only TGW6 was not under selection for the modern Taiwan temperate japonica rice accessions. For other groups, only a few genes showed significant selection; they are Gn1, qSH1 and qSW5 genes for V1; Bh4, Lg1, OsC1, Prog1 and TGW6 genes for V2; RAE2 gene for V6; Prog1 and qSH1 genes for V7; and An1, An2, Bh4, Edh1 and Waxy genes for V8. There was no significant selection for V3 and V5 among the 20 genes tested. Both groups include relatively primitive indica accessions in Taiwan. Thus, the genetic diversity has changed during cultivation and differs according to population. Table 4 Selection swept analysis of some domestication- or adaption-related genes of Taiwan rice accessions. The gene region and the nearby ± 1 Mb were used for the calculation. Only significant traits/groups are listed. Gene Group classification Number of sequences π θw Tajima's D An1 V4 73 0.07522 0.20383 -2.21879** An1 V8 61 0.10125 0.21108 -1.86562* An2 V4 73 0.03095 0.20471 -2.98748*** An2 V8 61 0.04019 0.21324 -2.90897*** Bh4 V2 17 0.10986 0.24517 -2.39274*** Bh4 V4 73 0.04551 0.20470 -2.73676*** Bh4 V8 61 0.08955 0.21322 -2.07901* Cold1 V4 73 0.06909 0.20456 -2.33085** Ehd1 V4 73 0.03862 0.20563 -2.85917*** Ehd1 V8 61 0.05927 0.21174 -2.58027*** Gn1 V1 40 0.06544 0.13948 -1.99547* Gn1 V4 73 0.04106 0.20555 -2.81393*** Hd3a V4 73 0.05331 0.20573 -2.60790*** IPA1 V4 73 0.08698 0.20552 -2.02404* Lg1 V2 17 0.10085 0.23332 -2.46130*** Lg1 V4 73 0.04990 0.20573 -2.66412*** OsC1 V2 17 0.14947 0.26621 -1.90065* OsC1 V4 73 0.05047 0.20573 -2.65666*** OsLg1 V4 73 0.07352 0.20399 -2.25074** Phr1 V4 73 0.09719 0.20335 -1.83741* Prog1 V2 17 0.11562 0.27046 -2.48232*** Prog1 V4 73 0.07806 0.20573 -2.17197** Prog1 V7 16 0.14808 0.30137 -2.23620** qSh1 V1 40 0.05931 0.23421 -2.81371*** qSh1 V4 73 0.03236 0.20561 -2.96598*** qSh1 V7 16 0.15545 0.29526 -2.08093* qSW5 V1 40 0.10905 0.23309 -2.00318* qSW5 V4 73 0.07536 0.2057 -2.23050** RAE2 V4 73 0.04642 0.20541 -2.71068*** RAE2 V7 44 0.04697 0.16912 -2.68728*** Rc V4 73 0.06071 0.20573 -2.48110** TGW6 V2 17 0.15465 0.2954 -2.06686* TT1 V4 73 0.03979 0.20409 -2.83281*** Wx V4 73 0.03674 0.20573 -2.89097*** Wx V8 61 0.09809 0.21346 -1.93567* Heading date 1 allele analysis showed that some indigenous rice accessions came from nearby regions Rice is a short-day plant and was domesticated in China (a temperate zone), then was brought to subtropical and tropical zones with warmer temperature and different photoperiods. The early rice plants that grew in a temperate region fitted the daylength atmosphere very well: they flowered (also known as heading) during early autumn and were ready to be harvested about 40 days later. However, when the plants were brought to the southern region with short daylength, the reduced vegetative growth period before heading would lead to decreased yield. Many reviews provided detailed information on the regulation of rice flowering and production (e.g., Itoh and Izawa 2013; Lee and An 2015; Tsuji et al . 2013). Mutations leading to the null function of sensitivity-to-photoperiod genes would increase crop yield because rice could grow in 2 or 3 seasons instead of only one each year and also reduce stress damage caused by seasonal typhoons, monsoons or drought. Thus, such a trait could be selected out in subtropical and tropical regions. Cultivated rice varieties and landraces exhibited large variation in flowering time, so rice heading behavior was controlled by quantitative trait loci (QTL). For instance, by using the progeny derived from a single cross between one japonica (Nipponbare) and one aus (Kasalath) line, researchers identified 15 QTL for the Heading date ( Hd ) trait (Yano et al. 2000). Hd1 was one of the most important loci to control rice flowering time and was identified as an Arabidopsis CO ortholog (Yano et al. 2000). By using the information from many local accessions (Takahashi et al. 2009) and the rice 3K project information (Wu et al. 2020a), about 10 Hd1 loss-of-function (LOF) alleles were identified (Yano et al. 2000; Takahashi et al. 2009; Wu et al. 2020a). The rice accessions with any of these LOF hd1 alleles would not be sensitive to photoperiod and thus could flower and mature after proper vegetative growth. Many landraces and most modern varieties in subtropical and tropical regions contained these alleles because they could adapt to the environment well and have high yield. Phylogenetic and haplotype network analysis of several of these alleles revealed that type 7 hd1 LOF mutation occurred in indica rice in insular areas in SEA, followed by introgression and expansion (i.e., brought by human beings) to nearby regions including the Indochina area and Indian subcontinent (Wu et al. 2020a). With a similar strategy and dataset, the results also suggested that type 13 mutation occurred in japonica rice in insular areas in SEA, followed by introgression and expansion of both japonica and indica accessions to nearby regions. In addition, some other hd1 LOF alleles were specific to local regions: type 3 was indica -specific and mainly from China, and type 19 was japonica -specific and mainly from Taiwan (Wu et al. 2020a). Data mining analysis of the 129 Taiwan indigenous rice accessions in the current study indicated that 6 contained type 13 hd1 alleles, including 5 japonica accessions and one indica . In addition, 5 indica accessions had type 7 alleles, 14 japonica accessions had the type 19 hd1 allele, and 3 indica accessions had the type 3 allele. Thus, the variations in the hd1 allele type revealed that some of the early rice cultivated in Taiwan came from China and mainland or insular SEA. There must have been intensive exchanges of rice accessions in Taiwan with the nearby regions a long time ago. Discussion In the current study, we performed a detailed analysis of the population structure changes in rice in Taiwan over thousands of years. Multidiscipline strategies including archaeological, morphological, genetic and genomic approaches were used. The materials included carbonized seeds excavated from central or southern Taiwan from 5000 years ago and those cultivated in indigenous villages or plain regions recently. We discuss which rice types arrived Taiwan in ancient times, any exchange of rice lines with nearby regions a long time ago, why there were major changes in the rice population in the last century as well as how domestication- and adaptation-related genes changed in different populations. Finally, we showed factors that have shaped the population structure of Taiwan rice accessions over these years. Traditional Taiwan cereals were present 5000 years ago Rice, foxtail millet and proso millet grains were excavated in southern Taiwan around 5000 BP in large quantity (Tsang et al. 2017). Multidiscipline analyses on indigenous habitat, linguistic divisions, archaeological remains, etc. were applied to search the early origin of Austronesian. Many studies proposed that the Formosan peoples and culture traits came from southern China by using archaeological data (Ferrell 1966; Bellwood 1997; Chang 1989; Deng et al. 2022; Tsang 2005) or language (Bellwood 1979; Ferrell 1969). Alternatively, our recent study provided difference hypothesis. We performed a multidisciplinary analysis from the viewpoint of archaeology, linguistics, and genome sequence as well as seed morphology to reveal early agriculture in Taiwan (Sagart et al. 2018). By using sequence information for several domestication-related genes, we found that the functional nucleotide polymorphisms of indigenous rice lines were the same as modern japonica and indica rice varieties elsewhere in the world. Thus, the early rice that arrived in Taiwan long time ago was already domesticated and was japonica (no indica rice in eastern Asia yet during that period). Indica rice arrived in Taiwan rather late, with some modern traits. With the botanically informed linguistic fieldwork of the agricultural vocabulary of indigenous villages, along with the earlier findings in archaeology, genetics and historical linguistics, early Taiwan agriculture was found to be based on foxtail millet, broomcorn millet and rice (Hsieh et al. 2011; Tsang et al. 2017). Together, we proposed the pre-Austronesians expanded south along the coast from Northern China 5000 BCE to reach northwest Taiwan in the second half of the 4th millennium BP (Sagart et al. 2018). The archaeological studies indicated that there were continuous rice cultivations in Taiwan from about 5000 years ago to the present time. By using 100 carbonized rice seeds excavated from 4 different sites with a time span from 5000 to 500 BP in southern Taiwan and 1300 BP in central Taiwan, we showed that rice seed size had changed over thousands of years, from a relatively small and round shape to a large and oblonga shape (Fig. 1 ). Previously we described the seed length, width and grain length/width (l/w) ratio of carbonized rice grains excavated from 18 sites in southern Taiwan (Table 1 , Hsu et al 2019. The time span ranged from 5000 BP to 300 BP, and the seed size also showed a huge change during the ~ 5000 years: seed length average 4.72 mm, width 2.52, and l/w ratio 1.88. This analysis again demonstrated that the seeds were small and round before 3000 BP and then became large and long later on. By using the excavated rice seed morphology, there must have been movement of rice between Taiwan and the nearby regions for thousands of years. Using the seed size information, the large seeds might be from SEA, such as Funan, Langkasuka, Salakanagara, Tarumanagara or Champa during that time. Studies of excavated rice grain indicated the changes in early cultivated rice of Taiwan In the current study, we measured the grain size of hundreds of carbonized rice seeds excavated from 4 sites in central or southern Taiwan (Fig. 1 , Table S5 ). Most rice grains recovered from excavated sites worldwide were preserved by carbonization, a process in which the organic structure was converted into inorganic carbon by heating (Wright 2003). The high temperature could lead to warping, shrinking or fracturing, although the seeds would not be destroyed by microbe decay (Wright 2003). This carbonization process could affect the length and width of rice grains (Ahn 1993). To differentiate japonica or indica carbonized rice seeds, the l/w ratio was used in most studies. Some researchers assume a uniform 20% shrinkage rate for the l/w ratio in the studies of all archaeological carbonized seeds (e.g., Fuller et al 2008; Fuller et al 2009; Harvey 2007. Table S5 illustrates the average, minimum and maximum values of seed length, width and l/w values for NKLE, YHF, WCT and HLL. Using the 20% shrinkage rate, the mean l/w values were 1.98, 2.29, 2.57, and 2.70 for the 4 sites. Information on many agronomic traits, including seed length and width, from the 3K rice project is available from the Rice SNP-Seek website of IRRI ( https://snp-seek.irri.org/ ). Using the traditional accessions (1048 lines) only, the l/w ratios were 3.05, 2.61, 3.31, 2.80, 3.06, 2.90, 2.17, 2.64 and 2.64 for aromatic , aus , ind 1A, ind 1B, ind 2, ind 3, temperate japonica , tropical japonica and subtropical japonica , respectively. Thus, the very early rice lines that may have been cultivated in Taiwan before 3800 BP (NKLE and YHF) were temperate japonica type. Since about 1500 BP (WCT and HLL), there were subtropical and tropical japonica as well as indica rice types according to the higher l/w values. This hypothesis coincided with the classification of the indigenous upland rice accessions: some primitive temperate japonica (V1 group) belong to the earliest type that arrived in Taiwan a long time ago. Complicated exchange with nearby regions before the late Ming Dynasty Many ornaments and tools excavated from eastern Taiwan since ~ 3000 BP were made of Fengtian jade (Hung et al. 2007). More than 100 sites dating from the early Neolithic to the Iron Age revealed an intensive jade production/industry in eastern Taiwan during that period. Electron probe microanalysis revealed that Fengtian jade was also present in excavated sites in the Philippines, Indonesia, Vietnam, Cambodia, Thailand, Malaysia and southern China (Hung et al. 2007; Hung et al. 2013; Alam et al. 2021). Therefore, there was frequent cultural contact between Taiwan and the insular areas as well as mainland SEA. With the extensive sea-based trade networks in the prehistoric world, rice seeds would accompany other crops. The route of early japonica rice dispersal to Taiwan, the Philippines and other SEA areas was reconstructed using the whole-genome resequencing of landraces (Alam et al. 2021). The japonica component of the Taiwanese indigenous rice accessions consisted of two distinct populations, including a result of admixture between temperate japonica that presumably came from northeast Asia and tropical japonica from the northern Philippines and mainland SEA (Alam et al 2021). In the current study, we also illustrated that some indigenous rice lines with different hd1 LOF alleles were brought to Taiwan from mainland and insular SEA as well as China during the early time. Thus, there was a complicated exchange in Taiwan rice accessions with nearby regions before the late Ming Dynasty (arrival of the Han people). Rice landraces in Taiwan provide good genetic resources for future breeding In the current study, some of the Taiwan rice landraces, including indigenous and Ming-Ching ones, are highly resistant to abiotic stresses such as drought or flooding (Fig. 2 and Figure S1 ), specifically the indigenous rice accessions that were cultivated in an upland practice at higher altitudes for thousands of years. In a genome-wide study of Asian japonica landraces, several selection sweeps occurred across 12 chromosomes. The one in the long arm of chromosome 1 was due to some Taiwan indigenous rice lines, and the peak coincided with genes associated with UV tolerance (Alam et al. 2021). Therefore, these lines were resistant to several stress treatments, and they all contained good traits ready for breeding. Climate change in recent years has caused serious problems worldwide, including to agricultural production. Problems include flooding, drought, heat, chilling, high UV, etc. Taiwanese indigenous peoples and traditional farmers have kept the rice landraces for hundreds and up to thousands of years. With many old traits preserved, they are good resources for future breeding programs. Abbreviations Nan-kuan-li East, NKLE; Youhsienfang, YHF; Wuchiantsuo, WCT; Huilaili, HLL; Taiwan Agricultural Research Institute, TARI; National Plant Genetic Resources Center, NPGRC; southeast Asia, SEA; Dee Geo Woo Gen, DGWG Declarations Acknowledgements We would like to acknowledge our gratitude to the Taiwanese indigenous peoples and traditional farmers for their stewardship of traditional rice landraces. We thank Ms. Lie-Hong Wu for maintaining greenhouse plants. We also thank Laura Smales (BioMedEditing, Toronto, Canada) for English editing. Funding This work was supported by the MOST grants 110-2313-B-001-005 and 109-2313-B-001-008 to YIH as well as ITAR grants AS-ITAR-110-TD06, AS-109-ITAR-TD08 and AS-108-ITAR-TD08 to THDH, SMY and YIH. Data Availability The data underlying this article are available in the NCBI Short Read Archive (SRA) database (project accessions nos. PRJNA485658, PRJNA373799, PRJNA623980, and PRJEB6180). Authors’ contributions YICH conceived and designed the study, CCW, CKL and LTH generated sequencing data. YHW, YCT, TFH and YTT analyzed the carbonized grains. YCT, NCD, JCL, DPS, CWW, MHL, DHW, SC, YPW and SJC collected rice accessions. CCW, CKL, FJW performed bioinformatics analysis. CHT, KTL, WLC provided archaeological materials. THDH, SMY and LS participated in frequent discussions. YICH wrote the manuscript with input from all authors. References 3KRGP (2014) The 3,000 Rice Genomes Project. GigaScience 3 (1):2047-2217X-2043-2047 Ahn S-M (1993) Origin and Differentiation of Domesticated Rice in Asia-Review of Archaeological and Botanical Evidences. University of London, University College London (United Kingdom), Alam O, R M Gutaker, C-C Wu, K A Hicks, K Bocinsky, C C Castillo, S Acabado, D Fuller, J A d’Alpoim Guedes, Y-I Hsing, M D Purugganan (2021) Genome Analysis Traces Regional Dispersal of Rice in Taiwan and Southeast Asia. Molecular Biology and Evolution 38 (11):4832-4846. doi:10.1093/molbev/msab209 Ashikari M, H Sakakibara, S Lin, T Yamamoto, T Takashi, A Nishimura, E R Angeles, Q Qian, H Kitano, M Matsuoka (2005) Cytokinin Oxidase Regulates Rice Grain Production. Science 309 (5735):741-745. doi:10.1126/science.1113373 Bellimod P (2004) The Origins and Dispersals of Agricultural Communities in Southeast Asia. Southeast Asia: from prehistory to history :21-40 Bellwood P (1979) Man's Conquest of the Pacific: The Prehistory of Southeast Asia and Oceania. New York: Oxford Univ. Press.· 1985. Prehistory of the Indo-Malaysianarchipelago. New York: Academic Press, Bellwood P (1997) Prehistory of the Indo-Malaysian Archipelago. Honolulu. University of Hawaii Press(First edition published 1985 by Academic Press, Sydney) INDO-PACIFIC PREHISTORY ASSOCIATION BULLETIN 23:2003 Bellwood P (2023) First Farmers: The Origins of Agricultural Societies. John Wiley & Sons, Bessho-Uehara K, D R Wang, T Furuta, A Minami, K Nagai, R Gamuyao, K Asano, R B Angeles-Shim, Y Shimizu, M Ayano, N Komeda, K Doi, K Miura, Y Toda, T Kinoshita, S Okuda, T Higashiyama, M Nomoto, Y Tada, H Shinohara, Y Matsubayashi, A Greenberg, J Wu, H Yasui, A Yoshimura, H Mori, S R McCouch, M Ashikari (2016) Loss of Function at Rae2, a Previously Unidentified Epfl, Is Required for Awnlessness in Cultivated Asian Rice. Proc Natl Acad Sci U S A 113 (32):8969-8974. doi:10.1073/pnas.1604849113 Blust R (1995) The Prehistory of the Austronesian-Speaking Peoples: A View from Language. Journal of World prehistory 9 (4):453-510 Castillo C C, K Tanaka, Y-I Sato, R Ishikawa, B Bellina, C Higham, N Chang, R Mohanty, M Kajale, D Q Fuller (2016) Archaeogenetic Study of Prehistoric Rice Remains from Thailand and India: Evidence of Early Japonica in South and Southeast Asia. Archaeological and Anthropological Sciences 8 (3):523-543. doi:10.1007/s12520-015-0236-5 Chang K-c (1989) Taiwan Archaeology in Pacific Perspective. In Chang, K. C., Li, K. C., Wolf, A. P., and Yin, A. C. (Eds.). Anthropological Studies of the Taiwan Area: Accomplishments and Prospects, Taipei: Department of Anthropology, National Taiwan University :87-97 Chu W L (2016) Rescue Excavation Report of the Anhelu Site. Taichung: National Museum of Natural Science (in Chinese) DAFTPG (1989) The History of Taiwan Rice Development and Production. Department of Agriculture and Forestry of the Taiwan Provincial Government (DAFTPG) (in Chinese) :837 Danecek P, A Auton, G Abecasis, C A Albers, E Banks, M A DePristo, R E Handsaker, G Lunter, G T Marth, S T Sherry (2011) The Variant Call Format and Vcftools. Bioinformatics 27 (15):2156-2158 Deng Z, S-c Kuo, M T Carson, H-c Hung (2022) Early Austronesians Cultivated Rice and Millet Together: Tracing Taiwan's First Neolithic Crops. Frontiers in Plant Science :2393 Deng Z, L Qin, Y Gao, A R Weisskopf, C Zhang, D Q Fuller (2015) From Early Domesticated Rice of the Middle Yangtze Basin to Millet, Rice and Wheat Agriculture: Archaeobotanical Macro-Remains from Baligang, Nanyang Basin, Central China (6700–500 Bc). PLoS One 10 (10):e0139885 Doi K, T Izawa, T Fuse, U Yamanouchi, T Kubo, Z Shimatani, M Yano, A Yoshimura (2004) Ehd1, a B-Type Response Regulator in Rice, Confers Short-Day Promotion of Flowering and Controls Ft-Like Gene Expression Independently of Hd1. Genes Dev 18 (8):926-936. doi:10.1101/gad.1189604 Edgar R C (2004a) Muscle: A Multiple Sequence Alignment Method with Reduced Time and Space Complexity. BMC Bioinformatics 5 (1):113 Edgar R C (2004b) Muscle: Multiple Sequence Alignment with High Accuracy and High Throughput. Nucleic acids research 32 (5):1792-1797 Ferrell R (1966) The Formosan Tribes, a Preliminary Linguistic Archaeological and Cultural Synthesis. na, Ferrell R (1969) Taiwan Aboriginal Groups: Problems in Cultural and Linguistic Classification. Institute of Ethnology. Academia Sinica Monograph 17 Fuller D, L Qin, E Harvey (2009) An Evolutionary Model for Chinese Rice Domestication: Reassessing the Data of the Lower Yangtze Region. New Approaches to Prehist Agric :312-345 Fuller D Q, L Qin, E Harvey (2008) A Critical Assessment of Early Agriculture in East Asia, with Emphasis on Lower Yangzte Rice Domestication. Pragdhara 18:17-52 Fuller D Q, Y-I Sato, C Castillo, L Qin, A R Weisskopf, E J Kingwell-Banham, J Song, S-M Ahn, J Van Etten (2010) Consilience of Genetics and Archaeobotany in the Entangled History of Rice. Archaeological and Anthropological Sciences 2 (2):115-131 Garris A J, T H Tai, J Coburn, S Kresovich, S McCouch (2005) Genetic Structure and Diversity in Oryza Sativa L. Genetics 169 (3):1631-1638. doi:10.1534/genetics.104.035642 Gu B, T Zhou, J Luo, H Liu, Y Wang, Y Shangguan, J Zhu, Y Li, T Sang, Z Wang, B Han (2015) An-2 Encodes a Cytokinin Synthesis Enzyme That Regulates Awn Length and Grain Production in Rice. Mol Plant 8 (11):1635-1650. doi:10.1016/j.molp.2015.08.001 Harvey E L (2007) Early Agricultural Communities in Northern and Eastern India: An Archaeobotanical Investigation. University of London, University College London (United Kingdom), Hill C, P Soares, M Mormina, V Macaulay, D Clarke, P B Blumbach, M Vizuete-Forster, P Forster, D Bulbeck, S Oppenheimer (2007) A Mitochondrial Stratigraphy for Island Southeast Asia. The American Journal of Human Genetics 80 (1):29-43 Hsieh J-s, Y-i C Hsing, T-f Hsu, P J-k Li, K-t Li, C-h Tsang (2011) Studies on Ancient Rice—Where Botanists, Agronomists, Archeologists, Linguists, and Ethnologists Meet. Rice 4 (3-4):178-183. doi:10.1007/s12284-011-9075-x Hsu T, Y Wang, B Fang, Y Chen, Y Tsai, Z Xie, Y-I Hsing (2019) A Comparative Study Onmorphological Types of Carbonized Rice Grains in Prehistorical Taiwan. (Chinese with English Abstract). Field Archaeology of Taiwan 19:55-86 Hua L, D R Wang, L Tan, Y Fu, F Liu, L Xiao, Z Zhu, Q Fu, X Sun, P Gu, H Cai, S R McCouch, C Sun (2015) Laba1, a Domestication Gene Associated with Long, Barbed Awns in Wild Rice. Plant Cell 27 (7):1875-1888. doi:10.1105/tpc.15.00260 Huang H (1984) Report for the Rescue Excavation of the Chi-Shan-Yen Site. Taipei City Archives (in Chinese) Huang Y-F, D-H Wu, C-L Wang, P-R Du, C-Y Cheng, C-C Cheng (2021) Survey of Rice Production Practices and Perception of Weedy Red Rice (Oryza Sativa F. Spontanea) in Taiwan. Weed Science 69 (5):526-535 Hung H-C, Y Iizuka, P Bellwood, K D Nguyen, B Bellina, P Silapanth, E Dizon, R Santiago, I Datan, J H Manton (2007) Ancient Jades Map 3,000 Years of Prehistoric Exchange in Southeast Asia. Proceedings of the National Academy of Sciences 104 (50):19745-19750 Hung H-c, K D Nguyen, P Bellwood, M T Carson (2013) Coastal Connectivity: Long-Term Trading Networks across the South China Sea. The Journal of Island and Coastal Archaeology 8 (3):384-404 IRGSP (2005) The Map-Based Sequence of the Rice Genome. Nature 436 (7052):793-800. doi:10.1038/nature03895 Ishii T, K Numaguchi, K Miura, K Yoshida, P T Thanh, T M Htun, M Yamasaki, N Komeda, T Matsumoto, R Terauchi, R Ishikawa, M Ashikari (2013) Oslg1 Regulates a Closed Panicle Trait in Domesticated Rice. Nat Genet 45 (4):462-465, 465e461-462. doi:10.1038/ng.2567 Ishimaru K, N Hirotsu, Y Madoka, N Murakami, N Hara, H Onodera, T Kashiwagi, K Ujiie, B Shimizu, A Onishi, H Miyagawa, E Katoh (2013) Loss of Function of the Iaa-Glucose Hydrolase Gene Tgw6 Enhances Rice Grain Weight and Increases Yield. Nat Genet 45 (6):707-711. doi:10.1038/ng.2612 Iso E (1944) Lectures on Rice Cultivating in Formosa [Taiwan]. Itoh H, T Izawa (2013) The Coincidence of Critical Day Length Recognition for Florigen Gene Expression and Floral Transition under Long-Day Conditions in Rice. Molecular plant 6 (3):635-649 Jin J, W Huang, J P Gao, J Yang, M Shi, M Z Zhu, D Luo, H X Lin (2008) Genetic Control of Rice Plant Architecture under Domestication. Nat Genet 40 (11):1365-1369. doi:10.1038/ng.247 Kawahara Y, M de la Bastide, J P Hamilton, H Kanamori, W R McCombie, S Ouyang, D C Schwartz, T Tanaka, J Wu, S Zhou (2013) Improvement of the Oryza Sativa Nipponbare Reference Genome Using Next Generation Sequence and Optical Map Data. Rice 6:1-10 Khush G S (1995) Modern Varieties—Their Real Contribution to Food Supply and Equity. Geojournal 35 (3):275-284 Khush G S (1999) Green Revolution: Preparing for the 21st Century. Genome 42 (4):646-655 Kiang Y (1979) The Extinction of Wild Rice (Oryza Perennis Formosana) in Taiwan. J Asian Ecol 1:1-9 Konishi S, T Izawa, S Y Lin, K Ebana, Y Fukuta, T Sasaki, M Yano (2006) An Snp Caused Loss of Seed Shattering During Rice Domestication. Science 312 (5778):1392-1396. doi:10.1126/science.1126410 Lee Y-S, G An (2015) Regulation of Flowering Time in Rice. J Plant Biol 58:353-360 Li H, B Handsaker, A Wysoker, T Fennell, J Ruan, N Homer, G Marth, G Abecasis, R Durbin (2009) The Sequence Alignment/Map Format and Samtools. Bioinformatics 25 (16):2078-2079 Li X-M, D-Y Chao, Y Wu, X Huang, K Chen, L-G Cui, L Su, W-W Ye, H Chen, H-C Chen (2015) Natural Alleles of a Proteasome Α2 Subunit Gene Contribute to Thermotolerance and Adaptation of African Rice. Nat Genet 47 (7):827-833 Liu Y (2011) From Siliao Excavated Site to Niao-Sung Culture Settlement. In: Report for Siliao Archaeological Site Rescue Excavation :1-24 Lu Z, H Yu, G Xiong, J Wang, Y Jiao, G Liu, Y Jing, X Meng, X Hu, Q Qian (2013) Genome-Wide Binding Analysis of the Transcription Activator Ideal Plant Architecture1 Reveals a Complex Network Regulating Rice Plant Architecture. The Plant Cell 25 (10):3743-3759 Luo J, H Liu, T Zhou, B Gu, X Huang, Y Shangguan, J Zhu, Y Li, Y Zhao, Y Wang, Q Zhao, A Wang, Z Wang, T Sang, Z Wang, B Han (2013) An-1 Encodes a Basic Helix-Loop-Helix Protein That Regulates Awn Development, Grain Size, and Grain Number in Rice. Plant Cell 25 (9):3360-3376. doi:10.1105/tpc.113.113589 Ma Y, X Dai, Y Xu, W Luo, X Zheng, D Zeng, Y Pan, X Lin, H Liu, D Zhang, J Xiao, X Guo, S Xu, Y Niu, J Jin, H Zhang, X Xu, L Li, W Wang, Q Qian, S Ge, K Chong (2015) Cold1 Confers Chilling Tolerance in Rice. Cell 160 (6):1209-1221. doi:10.1016/j.cell.2015.01.046 Matsuo T, K Hoshikawa (1993) Science of the Rice Plant: Morphology. In, vol 1. Food and Agriculture Policy Research Center, p 686 Rozas J, A Ferrer-Mata, J C Sánchez-DelBarrio, S Guirao-Rico, P Librado, S E Ramos-Onsins, A Sánchez-Gracia (2017) Dnasp 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Molecular biology and evolution 34 (12):3299-3302 Sagart L (2011) How Many Independent Rice Vocabularies in Asia? Rice 4:121-133 Sagart L, T-F Hsu, Y-C Tsai, C-C Wu, L-T Huang, Y-C Chen, Y-F Chen, Y-C Tseng, H-Y Lin, Y-i C Hsing (2018) A Northern Chinese Origin of Austronesian Agriculture: New Evidence on Traditional Formosan Cereals. Rice 11 (1):1-16 Saitoh K, K Onishi, I Mikami, K Thidar, Y Sano (2004) Allelic Diversification at the C (Osc1) Locus of Wild and Cultivated Rice: Nucleotide Changes Associated with Phenotypes. Genetics 168 (2):997-1007. doi:10.1534/genetics.103.018390 Sasaki A, M Ashikari, M Ueguchi-Tanaka, H Itoh, A Nishimura, D Swapan, K Ishiyama, T Saito, M Kobayashi, G S Khush (2002) A Mutant Gibberellin-Synthesis Gene in Rice. Nature 416 (6882):701-702 Shomura A, T Izawa, K Ebana, T Ebitani, H Kanegae, S Konishi, M Yano (2008) Deletion in a Gene Associated with Grain Size Increased Yields During Rice Domestication. Nat Genet 40 (8):1023-1028. doi:10.1038/ng.169 Silva F, A Weisskopf, C Castillo, C Murphy, E Kingwell-Banham, L Qin, D Q Fuller (2018) A Tale of Two Rice Varieties: Modelling the Prehistoric Dispersals of Japonica and Proto-Indica Rices. The Holocene 28 (11):1745-1758 Sweeney M T, M J Thomson, B E Pfeil, S McCouch (2006) Caught Red-Handed: Rc Encodes a Basic Helix-Loop-Helix Protein Conditioning Red Pericarp in Rice. The Plant Cell 18 (2):283-294. doi:10.1105/tpc.105.038430 Tajima F (1983) Evolutionary Relationship of DNA Sequences in Finite Populations. Genetics 105 (2):437-460 Tajima F (1989) Statistical Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism. Genetics 123 (3):585-595 Takahashi Y, K M Teshima, S Yokoi, H Innan, K Shimamoto (2009) Variations in Hd1 Proteins, Hd3a Promoters, and Ehd1 Expression Levels Contribute to Diversity of Flowering Time in Cultivated Rice. Proc Natl Acad Sci U S A 106 (11):4555-4560. doi:10.1073/pnas.0812092106 Tamaki S, S Matsuo, H L Wong, S Yokoi, K Shimamoto (2007) Hd3a Protein Is a Mobile Flowering Signal in Rice. Science 316 (5827):1033-1036 Teng Y (2003) Rice Industry Development and Its Future Prospects in Taiwan. Research Bulletin of Kaohsiung District Agricultural Research and Extension Station 14:1-23 Tsang C-H (2005) Recent Discoveries at the Tapenkeng Culture Sites in Taiwan: Implications for the Problem of Austronesian Origins. . In Laurent Sasgart, Roger Blench and Alicia Sanchez-Mazas, eds, The Peopling of East Asia (London: Routledge Curzon) :63-74 Tsang C-H, K-T Li, T-F Hsu, Y-C Tsai, P-H Fang, Y-I C Hsing (2017) Broomcorn and Foxtail Millet Were Cultivated in Taiwan About 5000 Years Ago. Botanical studies 58 (1):1-10 Tsuji H, K-i Taoka, K Shimamoto (2013) Florigen in Rice: Complex Gene Network for Florigen Transcription, Florigen Activation Complex, and Multiple Functions. Curr Opin Plant Biol 16 (2):228-235 Wang W, R Mauleon, Z Hu, D Chebotarov, S Tai, Z Wu, M Li, T Zheng, R R Fuentes, F Zhang, L Mansueto, D Copetti, M Sanciangco, K C Palis, J Xu, C Sun, B Fu, H Zhang, Y Gao, X Zhao, F Shen, X Cui, H Yu, Z Li, M Chen, J Detras, Y Zhou, X Zhang, Y Zhao, D Kudrna, C Wang, R Li, B Jia, J Lu, X He, Z Dong, J Xu, Y Li, M Wang, J Shi, J Li, D Zhang, S Lee, W Hu, A Poliakov, I Dubchak, V J Ulat, F N Borja, J R Mendoza, J Ali, J Li, Q Gao, Y Niu, Z Yue, M E B Naredo, J Talag, X Wang, J Li, X Fang, Y Yin, J C Glaszmann, J Zhang, J Li, R S Hamilton, R A Wing, J Ruan, G Zhang, C Wei, N Alexandrov, K L McNally, Z Li, H Leung (2018) Genomic Variation in 3,010 Diverse Accessions of Asian Cultivated Rice. Nature 557 (7703):43-49. doi:10.1038/s41586-018-0063-9 Wang Z Y, F Q Zheng, G Z Shen, J P Gao, D P Snustad, M G Li, J L Zhang, M M Hong (1995) The Amylose Content in Rice Endosperm Is Related to the Post‐Transcriptional Regulation of the Waxy Gene. The Plant Journal 7 (4):613-622 Watterson G (1975) On the Number of Segregating Sites in Genetical Models without Recombination. Theoretical population biology 7 (2):256-276 Wei F-J, Y-C Tsai, Y-M Hsu, Y-A Chen, C-T Huang, H-P Wu, L-T Huang, M-H Lai, L-Y Kuang, S-F Lo (2016a) Lack of Genotype and Phenotype Correlation in a Rice T-DNA Tagged Line Is Likely Caused by Introgression in the Seed Source. PLoS One 11 (5):e0155768 Wei F-J, Y-C Tsai, H-P Wu, L-T Huang, Y-C Chen, Y-F Chen, C-C Wu, Y-T Tseng, Y-I C Hsing (2016b) Both Hd1 and Ehd1 Are Important for Artificial Selection of Flowering Time in Cultivated Rice. Plant Sci 242:187-194 Wright P (2003) Preservation or Destruction of Plant Remains by Carbonization? J Archaeol Sci 30 (5):577-583 Wu C-C, C-K Liu, F-j Wei, L-T Huang, W-C Lin, Y-T Hsie, M-C Lin, C-H Chan, T-T Le, Y-P Wu, J-C Lo, H-F Li, M-H Lai, S Chen, A-L Hou, W-Y Chiou, S-M Yu, T-H D Ho, Y-I C Hsing (2022) A Rice Genomics and Phenomics Resource with Primarily Taiwan Rice Accessions (A Rice Genomics and Phenomics Resource with Primarily Taiwan Rice Accessions). Crop, Environment & Bioinformatics 18:12-36. doi:10.30061/ceb.202212_18.0002 Wu C-C, F-J Wei, W-Y Chiou, Y-C Tsai, H-P Wu, D Gotarkar, Z-H Wei, M-H Lai, Y-I C Hsing (2020a) Studies of Rice Hd1 Haplotypes Worldwide Reveal Adaptation of Flowering Time to Different Environments. PLoS One 15 (9):e0239028. doi:10.1371/journal.pone.0239028 Wu D H, D R Gealy, M H Jia, J D Edwards, M H Lai, A M McClung (2020b) Phylogenetic Origin and Dispersal Pattern of Taiwan Weedy Rice. Pest management science 76 (5):1639-1651 Wu I-L, T Lee, K Li, K-H Lee (2016) The Origin of Rice Cultivation at 4,000 Years Ago on the East Coast of Taiwan: Preliminary Results of Phytolith Analysis. Journal of Austronesain Studies 6 (1):25-50 Yano M, Y Katayose, M Ashikari, U Yamanouchi, L Monna, T Fuse, T Baba, K Yamamoto, Y Umehara, Y Nagamura (2000) Hd1, a Major Photoperiod Sensitivity Quantitative Trait Locus in Rice, Is Closely Related to the Arabidopsis Flowering Time Gene Constans. The Plant Cell 12 (12):2473-2483 Yu Y, T Tang, Q Qian, Y Wang, M Yan, D Zeng, B Han, C I Wu, S Shi, J Li (2008) Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication. Plant Cell 20 (11):2946-2959. doi:10.1105/tpc.108.060426 Zang Z, K Li (2015) Archaeological Heritage in the Tainan Science Park of Taiwan. National Museum of Prehistory, Zhu B F, L Si, Z Wang, Y Zhou, J Zhu, Y Shangguan, D Lu, D Fan, C Li, H Lin, Q Qian, T Sang, B Zhou, Y Minobe, B Han (2011) Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication. Plant Physiol 155 (3):1301-1311. doi:10.1104/pp.110.168500 Zhu Z, L Tan, Y Fu, F Liu, H Cai, D Xie, F Wu, J Wu, T Matsumoto, C Sun (2013) Genetic Control of Inflorescence Architecture During Rice Domestication. Nat Commun 4:2200. doi:10.1038/ncomms3200 Additional Declarations No competing interests reported. Supplementary Files TableS1excavatedsite.pdf Additional file 1: Table S1. The Chinese translation of the excavated sites and cultures used in the current study. TableS2accessions.xlsx Additional file 2: Table S2. Information about samples used in this study, including names, accession numbers of DNA, seed subtype information, and clustering results. TableS3genes.xlsx Additional file 3: Table S3. The 21 domestication- or adaptation-related genes used in the study. TableS4selectswept.xlsx Additional file 4: Table S4. Selection swept analysis of some domestication- or adaption-related genes of Taiwan rice accessions. The gene region and the nearby ± 1 Mb were used for the calculation. All traits/groups are listed. TableS5.pdf Additional file 5: Table S5. The size distribution of carbonated rice grain from the 4 excavated sites FigureS1.pdf Additional file 6: Figure S1.Seedling phenotype histograms of a japonica and an indica rice population under control or stress treatments. X-axis means phenotype and Y means % of the accessions used. Panels A and B, primary root length (in cm) of japonica and indica accessions under control condition, respectively; C and D, primary root length of japonica and indica accessions after 7-day flooding treatment, respectively; E and F, shoot length (in cm) of japonica and indica accessions under control condition, respectively; G and H, shoot length of japonica and indica accessions after 7-day flooding treatmenton, respectively; I and J, total root length (primary + all crown roots) of japonica and indica accessions under control condition, respectively; K and L, total root length of japonica and indica accessions after 7-day flooding treatment, respectively; M and N, total crown root length of japonica and indica accessions under control condition, respectively; O and P, total crown root length of japonica and indica accessions after 8-day 0.5 μM ABA treatment, respectively; Q and R, primary root length of japonica and indica accessions under control condition, respectively; S and T, primary root length of japonica and indica accessions after 8-day 0.5 μM ABA treatment, respectively; U and V, crown root number of japonica and indica accessions under control condition, respectively; W and X, crown root number of japonica and indica accessions after 8-day 0.5 μM ABA treatment, respectively; Y and Z, survival rate (as %) after 3-day 25% PEG treatment of japonica and indica accessions, respectively; AA and AB, the ratio of sheet length after7-day flooding treatment (compared with control) of japonica and indica accessions, respectively; AC and AD, the ratio (as %) of root length after 7-day flooding treatment (compared with control) of japonica and indica accessions, respectively; AE and AF, the ratio (as %) of total root length after 8-day 0.5 μM ABA treatment (compared with control) of japonica and indica accessions, respectively; AG and AH, the ratio (as %) of crown root length after 8-day 0.5 μM ABA treatment (compared with control) of japonica and indica accessions, respectively; AI and AJ, the ratio (as %) of primary root length after 8-day 0.5 μM ABA treatment (compared with control) of japonica and indica accessions, respectively; AK and AL, the ratio (as %) of crown root number after 8-day 0.5 μM ABA treatment (compared with control) of japonica and indica accessions, respectively. Blue means aboriginal rice accessions, green means Mingching landraces and orange modern varieties. Arrow indica te the positions of control variety Tainung67 or Taichung Native 1 for japonica or indica accessions, respectively. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-3218983","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":223074333,"identity":"24b2eba7-45d2-415e-9088-a633335d475e","order_by":0,"name":"Cheng-chieh Wu","email":"","orcid":"","institution":"Institute of Plant and Microbial Biology, Academia Sinica","correspondingAuthor":false,"prefix":"","firstName":"Cheng-chieh","middleName":"","lastName":"Wu","suffix":""},{"id":223074334,"identity":"0e0cdb78-9763-479b-a3d5-a1bc3523d0a9","order_by":1,"name":"Chun-Kai Liu","email":"","orcid":"","institution":"Institute of Plant and Microbial 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02:59:13","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-3218983/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-3218983/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":41175630,"identity":"0dca9c15-7589-4a66-af44-23d781d803ca","added_by":"auto","created_at":"2023-08-07 12:46:25","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":820116,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eCarbonated rice seed size variations from 4 excavated sites.\u003c/strong\u003e The distribution of seed length, width and thickness (in mm) of 100 seeds each site was shown. Green: Nankuanli East (NKLE), ~4800 BP at Tainan; purple: Youhsienfang (YHF), ~3800 BP at Tainan; cyan: Wuchiantsuo (WCT), ~1400-500 BP at Tainan; orange: Huilaili (HLL), ~1300 BP at Taichung.\u003c/p\u003e","description":"","filename":"Figure1.png","url":"https://assets-eu.researchsquare.com/files/rs-3218983/v1/c1eeffb4044eb920467e57fb.png"},{"id":41174954,"identity":"c9377a9b-2d5b-4913-a394-dd006790fe30","added_by":"auto","created_at":"2023-08-07 12:38:25","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":81959,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003ePhenotype histograms of a \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003ejaponica\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003e and an \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eindica\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003epopulation under stress treatments\u003c/strong\u003e. X-axis means root length (A and B) or the resistance rate (C and D, compared with control), and y-axis means % of the accessions used. Panels A and B, root length (cm) under 7-day flooding treatment of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e accessions, respectively; C and D, survival rate after 3-day 25% PEG treatment of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e accessions, respectively. Blue means aboriginal rice accessions, green means Mingching landraces and orange modern varieties. Arrow \u003cem\u003eindica\u003c/em\u003ete the positions of control variety Tainung67 or Taichung Native 1 for \u003cem\u003ejaponica\u003c/em\u003e or \u003cem\u003eindica\u003c/em\u003e accessions, respectively.\u003c/p\u003e","description":"","filename":"Figure2.png","url":"https://assets-eu.researchsquare.com/files/rs-3218983/v1/975d0e5c10dfc32756ac9d5b.png"},{"id":41906053,"identity":"ba64a33c-b32b-44dd-85c2-cb6a81bf9779","added_by":"auto","created_at":"2023-08-22 02:37:19","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1369060,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3218983/v1/6ecbe15f-e3d0-4788-be11-6f8b855888f7.pdf"},{"id":41174957,"identity":"d3bff00a-b3bb-4dd4-bdfa-5a0644ebe54b","added_by":"auto","created_at":"2023-08-07 12:38:25","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":85887,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eAdditional file 1: Table S1. \u003c/strong\u003eThe Chinese translation of the excavated sites and cultures used in the current study.\u003c/p\u003e","description":"","filename":"TableS1excavatedsite.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3218983/v1/f976bb38f61c37851b058d0c.pdf"},{"id":41175629,"identity":"dd86f45a-8048-41ec-ac0a-a9a5f807cdf3","added_by":"auto","created_at":"2023-08-07 12:46:25","extension":"xlsx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":22094,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eAdditional file 2: Table S2\u003c/strong\u003e. Information about samples used in this study, including names, accession numbers of DNA, seed subtype information, and clustering results.\u003c/p\u003e","description":"","filename":"TableS2accessions.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-3218983/v1/ecd657ce9e28456d8a7b8a98.xlsx"},{"id":41174956,"identity":"08bf0d4d-dc53-49a2-873f-1c87499c857d","added_by":"auto","created_at":"2023-08-07 12:38:25","extension":"xlsx","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":15877,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eAdditional file 3: Table S3\u003c/strong\u003e. The 21 domestication- or adaptation-related genes used in the study.\u003c/p\u003e","description":"","filename":"TableS3genes.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-3218983/v1/bef66eddf774b885f5bd6a3a.xlsx"},{"id":41174960,"identity":"f2dfec37-1589-4035-816b-def23a20c1c3","added_by":"auto","created_at":"2023-08-07 12:38:26","extension":"xlsx","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":30579,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eAdditional file 4: Table S4\u003c/strong\u003e. Selection swept analysis of some domestication- or adaption-related genes of Taiwan rice accessions. The gene region and the nearby ± 1 Mb were used for the calculation. All traits/groups are listed.\u003c/p\u003e","description":"","filename":"TableS4selectswept.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-3218983/v1/b256323004796bdd885e1e47.xlsx"},{"id":41175631,"identity":"af6c4604-eb1c-4fbf-bb64-bed9ebbd9517","added_by":"auto","created_at":"2023-08-07 12:46:26","extension":"pdf","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":106762,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eAdditional file 5: Table S5\u003c/strong\u003e. The size distribution of carbonated rice grain from the 4 excavated sites\u003c/p\u003e","description":"","filename":"TableS5.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3218983/v1/713b225b380f191d98119e67.pdf"},{"id":41175632,"identity":"932d95ea-4575-467c-9755-c6b6d0b7fa2e","added_by":"auto","created_at":"2023-08-07 12:46:26","extension":"pdf","order_by":6,"title":"","display":"","copyAsset":false,"role":"supplement","size":246008,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eAdditional file 6: Figure S1.\u003c/strong\u003eSeedling phenotype histograms of a \u003cem\u003ejaponica\u003c/em\u003eand an \u003cem\u003eindica\u003c/em\u003e rice population under control or stress treatments. X-axis means phenotype and Y means % of the accessions used. Panels A and B, primary root length (in cm) of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e accessions under control condition, respectively; C and D, primary root length of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e accessions after 7-day flooding treatment, respectively; E and F, shoot length (in cm) of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003eaccessions under control condition, respectively; G and H, shoot length of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e accessions after 7-day flooding treatmenton, respectively; I and J, total root length (primary + all crown roots) of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003eaccessions under control condition, respectively; K and L, total root length of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e accessions after 7-day flooding treatment, respectively; M and N, total crown root length of \u003cem\u003ejaponica\u003c/em\u003eand \u003cem\u003eindica\u003c/em\u003e accessions under control condition, respectively; O and P, total crown root length of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e accessions after 8-day 0.5 μM ABA treatment, respectively; Q and R, primary root length of \u003cem\u003ejaponica\u003c/em\u003eand \u003cem\u003eindica\u003c/em\u003e accessions under control condition, respectively; S and T, primary root length of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003eaccessions after 8-day 0.5 μM ABA treatment, respectively; U and V, crown root number of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e accessions under control condition, respectively; W and X, crown root number of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003eaccessions after 8-day 0.5 μM ABA treatment, respectively; Y and Z, survival rate (as %) after 3-day 25% PEG treatment of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003eaccessions, respectively; AA and AB, the ratio of sheet length after7-day flooding treatment (compared with control) of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003eaccessions, respectively; AC and AD, the ratio (as %) of root length after 7-day flooding treatment (compared with control) of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003eaccessions, respectively; AE and AF, the ratio (as %) of total root length after 8-day 0.5 μM ABA treatment (compared with control) of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e accessions, respectively; AG and AH, the ratio (as %) of crown root length after 8-day 0.5 μM ABA treatment (compared with control) of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e accessions, respectively; AI and AJ, the ratio (as %) of primary root length after 8-day 0.5 μM ABA treatment (compared with control) of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e accessions, respectively; AK and AL, the ratio (as %) of crown root number after 8-day 0.5 μM ABA treatment (compared with control) of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e accessions, respectively. Blue means aboriginal rice accessions, green means Mingching landraces and orange modern varieties. Arrow \u003cem\u003eindica\u003c/em\u003ete the positions of control variety Tainung67 or Taichung Native 1 for \u003cem\u003ejaponica\u003c/em\u003eor \u003cem\u003eindica\u003c/em\u003e accessions, respectively.\u003c/p\u003e","description":"","filename":"FigureS1.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3218983/v1/d89e641ebbe82d0adaf8a4c6.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Population structure dynamics of Taiwan rice accessions over thousands of years as revealed by archaeological, morphological and genome sequencing information","fulltext":[{"header":"Introduction","content":"\u003cp\u003eAsian cultivated rice (\u003cem\u003eOryza sativa\u003c/em\u003e) is one of the most important crops in the world and the most widely consumed. The rice was genetically divided into 2 main subspecies, \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e, with distinct morphological and physiological characteristics (reviewed by atsuo and Hoshikawa, 1993). Later on, with the analysis of molecular markers nd whole genome sequencing (3KRGP 2014), rice was found to contain 5 major subpopulations: \u003cem\u003eaus\u003c/em\u003e, \u003cem\u003eindica\u003c/em\u003e, temperate \u003cem\u003ejaponica\u003c/em\u003e, tropical \u003cem\u003ejaponica\u003c/em\u003e, and \u003cem\u003earomatic\u003c/em\u003e. In 2018, a detailed analysis of the 3K accessions further classified \u003cem\u003eindica\u003c/em\u003e rice into \u003cem\u003eind\u003c/em\u003e1a, \u003cem\u003eind\u003c/em\u003e1b, \u003cem\u003eind\u003c/em\u003e2 and \u003cem\u003eind\u003c/em\u003e3 and \u003cem\u003ejaponica\u003c/em\u003e rice into tropical, subtropical and temperate \u003cem\u003ejaponica\u003c/em\u003e (Wang \u003cem\u003eet al.\u003c/em\u003e 2018). According to archaeological studies, the early domesticated (i.e., non-shattering) cultivated rice in China was the \u003cem\u003ejaponica\u003c/em\u003e type, about 8,000 years ago, collected from Baligang in the Yellow River-Huai River-Plain (Deng \u003cem\u003eet al.\u003c/em\u003e 2015). Although there was rice collected from the Shangshan site about 9,000 years ago in the Lower Yangtze region (Liu et al. 2007; Zuo et al. 2017), most of them are still shattering. Wild rice ancestral to \u003cem\u003eindica\u003c/em\u003e was present in the northern Indian subcontinent before the arrival of non-shattering \u003cem\u003ejaponica\u003c/em\u003e (Silva \u003cem\u003eet al.\u003c/em\u003e 2018). \u003cem\u003eIndica\u003c/em\u003e rice was domesticated after the arrival of domesticated \u003cem\u003ejaponica\u003c/em\u003e rice, about 4,000 years ago, in the Ganges plains of eastern India (Fuller \u003cem\u003eet al.\u003c/em\u003e 2010). PCR amplification followed by sequencing of fragmented products using nuclear- and plastic- primers of hundreds of archaeological grains excavated from India (2 archaeological sites) and Thailand (4 sites) dated 2500 to 1500 before present (BP) revealed that the rice was predominantly \u003cem\u003ejaponica\u003c/em\u003e in Thailand and a mixture of \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e with \u003cem\u003eindica\u003c/em\u003e in the minority in India (Castillo \u003cem\u003eet al.\u003c/em\u003e 2016). Thus, the movement of \u003cem\u003eindica\u003c/em\u003e rice accessions to Southeast Asia (SEA) and East Asia (EA) was relatively late as compared with \u003cem\u003ejaponica\u003c/em\u003e rice cultivation.\u003c/p\u003e \u003cp\u003eAccording to the archaeological studies, there are thousands of carbonized rice grains found in Nan-kuan-li (NKL) and Nan-kuan-li East (NKLE) excavated sites in southern Taiwan. Ten \u003csup\u003e14\u003c/sup\u003eC dates obtained from these sites indicate that they were there between 5,000 to 4,500 BP. Other crop remains such as foxtail millet (\u003cem\u003eSetaria italica\u003c/em\u003e) and broomcorn millet (\u003cem\u003ePanicum miliaceum\u003c/em\u003e) as well as farming tools such as shell knives and stone hoes were discovered (Hsieh \u003cem\u003eet al.\u003c/em\u003e 2011; Tsang \u003cem\u003eet al.\u003c/em\u003e 2017). Thus, rice and millet farming may have been an important food source for people living about 5000 years ago in southern Taiwan.\u003c/p\u003e \u003cp\u003eTaiwan indigenous people are the original inhabitants of Taiwan. Their ancestors may have been living in Taiwan for thousands of years before the Han Chinese immigration began in the 17th century. Taiwanese aborigines are Austronesian-speaking peoples and were demonstrated as the origin of Austronesian languages located in the Philippines, Indonesia, Malaysia, Madagascar, Polynesia and Oceania (see e.g., Hill \u003cem\u003eet al\u003c/em\u003e 2007). The dispersal is presumed to have led to the spread of Austronesian languages, cultural similarities, and agriculture and so on (Blust 1995; Bellwood 1997; Bellimod 2004; Bellwood 2023). Thus, the Taiwanese indigenous people have played important roles as the bridge of the mainland and the Pacific, and the analyses of early agriculture are critical. According to this \u0026ldquo;Out-of-Taiwan\u0026rdquo; hypothesis, rice, millet and taro are the three among many others important for the dispersal. The linguistic studies also coincide well with the flow as most people, if not all, in this area called rice *pajay before Columbus\u0026rsquo; time (Sagart 2011).\u003c/p\u003e \u003cp\u003eThe population structure of domesticated rice species has been influenced by civilization, human migration, taste preference, plant introgression, etc., during the history of the cultivation. Since the 20th century, plant breeding programs have played critical roles in crop production; thus hybridization between parental cultivars with desirable traits followed by intensive artificial selection are important for the development of new varieties.\u003c/p\u003e \u003cp\u003eIn the current study, we used carbonized rice grains from several excavated sites in Taiwan to reveal the seed size changes across thousands of years on the island. We also used whole genome sequencing to reveal the population structure differences among the current Taiwan rice accessions with the view that 1) the early rice accessions in Taiwan had been cultivated for thousands of years, 2) rice cultivation changed with the arrival of the Han people about 400 years ago, 3) changes from \u003cem\u003eindica\u003c/em\u003e to \u003cem\u003ejaponica\u003c/em\u003e rice during the Japanese colonial period started about 100 years ago, and 4) the modern breeding period has existed since the early 20th century. The questions we asked included 1) Which type was the early rice that arrived in Taiwan in ancient times, 2) What are the reasons for changes in major rice populations, 3) What are the relationships in rice populations with the nearby regions, and 4) How did the domestication/adaptation alleles change in different populations. We show how civilization, human migration, taste preference, natural introgression and breeding programs have shaped the population structure of Taiwan rice accessions over thousands of years.\u003c/p\u003e"},{"header":"Materials and Methods","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eArchaeological materials\u003c/h2\u003e \u003cp\u003eHundreds of carbonized rice grains were collected from 4 excavated sites belonging to 4 cultures by using the floating method. The sites are NKLE (23\u0026ordm;6'58\"N, 120\u0026ordm;16'35\"E, altitude 0.5 m, 4800 BP) of the Dapenkeng culture (4800\u0026thinsp;\u0026minus;\u0026thinsp;3300 BP), Youhsienfang (YHF, 23\u0026deg;06'54.0\"N 120\u0026deg;16'25.0\"E, altitude 6 m) of the Niuchouzi culture (3800\u0026thinsp;\u0026minus;\u0026thinsp;3300 BP), Wuchiantsuo (WCT, 23\u0026deg;05'39.0\"N 120\u0026deg;16'25.0\"E, altitude 7 m) of the Niaosong culture (1400\u0026thinsp;\u0026minus;\u0026thinsp;500 BP), and Huilaili (HLL, 24\u0026ordm;09'42.8\"N, 120\u0026ordm;38'11.6\"E, altitude 73 m, 1300 BP) of the Fanziyuen culture (2000-400BP). In total, 100 carbonized rice samples from each site were used to estimate seed width, length and thickness by using a digital ruler (Mitutoyo Co., Japan) with accuracy of 0.01 mm. The Chinese translation of the excavated sites and cultures are listed in Table \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec4\" class=\"Section2\"\u003e \u003ch2\u003ePlant materials and growth condition\u003c/h2\u003e \u003cp\u003eThe seeds of the indigenous rice accessions, landraces and modern varieties were obtained from the National Plant Genetic Resources Center (NPGRC), Taiwan Agricultural Research Institute (TARI), Taiwan. The seeds were collected from the indigenous peoples of the mountain regions of different tribes. Part of the samples were collected around 1900 and the rest in recent years. The accession names for all seeds are in Table \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e. The plants of single seed descent were cultivated until tillering stage in an Academia Sinica greenhouse under natural light. Healthy leaves without insect damage from one single plant were harvested, frozen under liquid nitrogen and stored at -80℃ for DNA extraction.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec5\" class=\"Section2\"\u003e \u003ch2\u003eWhole genome sequencing and single nucleotide polymorphism (SNP) calling\u003c/h2\u003e \u003cp\u003eGenomic DNA was extracted from leaves by using a DNeasy Plant Mini Kit (Qiagen) following the manufacturer\u0026rsquo;s protocol. DNA was prepared for Illumina genome sequencing using the Illumina Hiseq2000 instrument with a 2 x 150-bp read configuration. A few of the Taiwan rice accessions were sequenced in the 3K rice project (3KRGP 2014). Sequencing data for these accessions are available from the NCBI Short Read Archive (Bioproject accession nos. PRJNA485658, PRJNA373799, PRJNA623980, and PRJEB6180).\u003c/p\u003e \u003cp\u003eThe paired reads were mapped against the Os-Nipponbare-Reference-IRGSP-1.0 database (IRGSP 2005; Kawahara \u003cem\u003eet al.\u003c/em\u003e 2013). SAMtools (Li \u003cem\u003eet al.\u003c/em\u003e 2009) and VCFtools (Danecek \u003cem\u003eet al.\u003c/em\u003e 2011) were used to handle the sequence alignment/map format (SAM) and variant call format (VCF) of the file. To detect SNPs and small indels, we used the command lines in the section \u0026ldquo;Variant Calling\u0026rdquo; in \u0026ldquo;Workflows\u0026rdquo; of the SAMtools manual. The information on SNPs and small indels was recorded in VCF files. The detailed methods were similar to those described previously (Wei \u003cem\u003eet al.\u003c/em\u003e 2016a; Wu \u003cem\u003eet al.\u003c/em\u003e 2020a).\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec6\" class=\"Section2\"\u003e \u003ch2\u003eScoring of grain-related traits\u003c/h2\u003e \u003cp\u003eSeveral grain-related traits were screened: long awn, red caryopsis, glutinous, seed width and seed length. Awns\u0026thinsp;\u0026gt;\u0026thinsp;2 cm were defined as long awns. Ground rice grain was treated with 0.2% iodine reagent and scored 5 min later for the glutinous (sticky) phenotype.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec7\" class=\"Section2\"\u003e \u003ch2\u003eEstimation of diversity of domestication- or adaptation-related genes\u003c/h2\u003e \u003cp\u003eTwenty domestication- or adaptation-related genes were used to evaluate the gene diversity. They are \u003cem\u003eAn1\u003c/em\u003e (Luo \u003cem\u003eet al.\u003c/em\u003e 2013), \u003cem\u003eAn2\u003c/em\u003e (Gu \u003cem\u003eet al.\u003c/em\u003e 2015; Hua \u003cem\u003eet al.\u003c/em\u003e 2015), \u003cem\u003eBh4\u003c/em\u003e (Zhu \u003cem\u003eet al.\u003c/em\u003e 2011), \u003cem\u003eCold1\u003c/em\u003e (Ma \u003cem\u003eet al.\u003c/em\u003e 2015), \u003cem\u003eEhd1\u003c/em\u003e (Doi \u003cem\u003eet al.\u003c/em\u003e 2004), \u003cem\u003eGn1\u003c/em\u003e (Ashikari \u003cem\u003eet al.\u003c/em\u003e 2005), \u003cem\u003eHd3a\u003c/em\u003e (Tamaki \u003cem\u003eet al.\u003c/em\u003e 2007), \u003cem\u003eIPA1\u003c/em\u003e (Lu \u003cem\u003eet al.\u003c/em\u003e 2013), \u003cem\u003eLg1\u003c/em\u003e (Zhu \u003cem\u003eet al.\u003c/em\u003e 2013), \u003cem\u003eOsLg1\u003c/em\u003e (Ishii \u003cem\u003eet al.\u003c/em\u003e 2013), \u003cem\u003eOsC1\u003c/em\u003e (Saitoh \u003cem\u003eet al.\u003c/em\u003e 2004), \u003cem\u003ePhr1\u003c/em\u003e (Yu \u003cem\u003eet al.\u003c/em\u003e 2008), \u003cem\u003eProg1\u003c/em\u003e (Jin \u003cem\u003eet al.\u003c/em\u003e 2008), \u003cem\u003eqSH1\u003c/em\u003e (Konishi \u003cem\u003eet al.\u003c/em\u003e 2006), \u003cem\u003eqSW5\u003c/em\u003e (Shomura \u003cem\u003eet al.\u003c/em\u003e 2008), \u003cem\u003eRAE2\u003c/em\u003e (Bessho-Uehara \u003cem\u003eet al.\u003c/em\u003e 2016), \u003cem\u003eRc\u003c/em\u003e (Sweeney \u003cem\u003eet al.\u003c/em\u003e 2006), \u003cem\u003eTGW6\u003c/em\u003e (Ishimaru \u003cem\u003eet al.\u003c/em\u003e 2013), \u003cem\u003eTT1\u003c/em\u003e (Li \u003cem\u003eet al.\u003c/em\u003e 2015) and \u003cem\u003eWaxy\u003c/em\u003e (Wang \u003cem\u003eet al.\u003c/em\u003e 1995). These genes are related to plant stature, grain phenotypes, temperature tolerance or photoperiod sensitivity. Detailed information for these genes is in Table \u003cspan refid=\"MOESM3\" class=\"InternalRef\"\u003eS3\u003c/span\u003e.\u003c/p\u003e \u003cp\u003eGenomic sequences were aligned by using MUSCLE (Edgar 2004a, b). The \u0026minus;\u0026thinsp;1 Mb to +\u0026thinsp;1 Mb region of each of these genes was used for the analysis. Statistical analysis involved using DNAsp.v6 (Rozas \u003cem\u003eet al.\u003c/em\u003e 2017). Items analyzed included number of polymorphic (segregating) sites (S), total number of mutations (Eta), average number of nucleotide differences (\u003cem\u003ek\u003c/em\u003e), nucleotide diversity (\u003cem\u003eπ\u003c/em\u003e) (Tajima 1983), theta (per sequence) from Eta \u003cem\u003eθ\u003c/em\u003e, and Watterson\u0026rsquo;s estimator of theta (per site) from Eta \u003cem\u003eθw\u003c/em\u003e (Watterson 1975). The neutrality test, with Tajima's \u003cem\u003eD\u003c/em\u003e value, was used to test the neutral mutation hypothesis (Tajima 1989). The \u003cem\u003eD\u003c/em\u003e value was based on the discrepancy between \u003cem\u003eπ\u003c/em\u003e and \u003cem\u003eθw\u003c/em\u003e; thus, negative values indicate excess low-frequency polymorphism.\u003c/p\u003e \u003c/div\u003e"},{"header":"Results","content":"\u003cdiv id=\"Sec9\" class=\"Section2\"\u003e \u003ch2\u003eContinuous rice cultivation in Taiwan from 5000 years ago\u003c/h2\u003e \u003cp\u003eThe earliest Taiwan carbonized rice grains were found in the excavated sites about 5000 years ago. Thousands of carbonized rice grains were found in NKL and NKLE in southern Taiwan from 5000\u0026thinsp;\u0026minus;\u0026thinsp;4500 BP (Hsieh \u003cem\u003eet al.\u003c/em\u003e 2011; Zang and Li 2015). Rice was found continuously in the southern part in YHF (3800\u0026thinsp;\u0026minus;\u0026thinsp;3300 BP, Zang and Li 2015), WCT (1800\u0026thinsp;\u0026minus;\u0026thinsp;500 BP, Zang and Li 2015) and Siliao (2300\u0026thinsp;\u0026minus;\u0026thinsp;600 BP, Liu 2011. There were also reports of early rice in Fushan (4500\u0026thinsp;\u0026minus;\u0026thinsp;3500 BP) and Chaolaiqiao (4500\u0026thinsp;\u0026minus;\u0026thinsp;3500 BP) during the middle Neolithic period in eastern Taiwan (Wu \u003cem\u003eet al.\u003c/em\u003e 2016; Deng \u003cem\u003eet al.\u003c/em\u003e 2022). In central Taiwan, early rice was found in Anhe (4800\u0026thinsp;\u0026minus;\u0026thinsp;4000 BP, Deng \u003cem\u003eet al.\u003c/em\u003e 2022) and HLL (1300 BP, Chu 2016). In northern Taiwan, carbonized rice grains were found in the Zhiwuyuan site (Taipei Botanical Garden) (4500 BP, Deng \u003cem\u003eet al\u003c/em\u003e. 2022) and Chishanyan site (4000\u0026thinsp;\u0026minus;\u0026thinsp;3000 BP, Huang 1984). Thus, archaeological studies indicated continuous rice cultivations in Taiwan from about 5000 years ago to the present.\u003c/p\u003e \u003cp\u003eUsing 100 carbonized seeds from 4 excavated sites, we studied the seed size changes by measuring the seed length, width and thickness. Figure\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e shows that early rice seeds were relatively small: with length 3 to 4.5 mm, width 1.8 to 2.9 mm and thickness 1.1 to 2 mm at NKLE and YHF, both located in southern Taiwan and before 3300 BP. The seed size variations during this period were rather small. For the seeds with a wide range of time (~\u0026thinsp;1400\u0026thinsp;\u0026minus;\u0026thinsp;500 BP) in the south (i.e., WCT), the length varied from 4.5 to 7 mm, width 2.2 to 3.6 mm and thickness 1.3 to 2.9 mm. Thus, the seed size was significantly larger than earlier ones and with large variation. Some of these seeds were double in size as compared with the two earlier ones. About the same time (1300 BP) in central Taiwan (i.e., HLL), seed length was 3.8 to 6 mm, width 1.8 to 3 mm, and thickness 1.2 to 2.1 mm. The seeds were larger than seeds from NKLE and YHF and smaller than those from WCT, again with large variation. Therefore, rice seed size in Taiwan has changed over thousands of years, from relatively small and round to large with an oblonga shape.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec10\" class=\"Section2\"\u003e \u003ch2\u003eTotal of 265 accessions were used in the current genomic study\u003c/h2\u003e \u003cp\u003eA total of 265 rice accessions collected in Taiwan were used in the study (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e, Table \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e). These included 129 accessions collected from indigenous villages, 58 belonging to those brought to Taiwan about 400 years ago, 17 breeding lines, 58 modern varieties and one weedy rice. In addition to these 263 lines, 2 wild rice accessions were collected in Ba-der, Taoyuan. All of the 263\u0026thinsp;+\u0026thinsp;2 accessions (listed in Table \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e) underwent whole genome sequencing followed by further analysis.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eThe subgroups of Taiwanese rice accessions used int the study. No \u003cem\u003eaus\u003c/em\u003e or \u003cem\u003earomatic\u003c/em\u003e types were found in local lines.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"7\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eTemperate\u003c/p\u003e \u003cp\u003e\u003cem\u003ejaponica\u003c/em\u003e\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eSubtropical\u003c/p\u003e \u003cp\u003e\u003cem\u003ejapopnica\u003c/em\u003e\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTropical\u003c/p\u003e \u003cp\u003e\u003cem\u003ejaponica\u003c/em\u003e\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cem\u003eindica\u003c/em\u003e\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003e\u003cem\u003eAdmixture\u003c/em\u003e\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003eTotal\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eIndigenous\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e58\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e12\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e39\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e129\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMingching\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e58\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e58\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eModern\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e54\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e75\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eRed rice (weedy)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003etotal\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e112\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e114\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e263\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec11\" class=\"Section2\"\u003e \u003cp\u003eSum: 263\u0026thinsp;+\u0026thinsp;2 wild relatives\u003c/p\u003e \u003cp\u003eMany rice landraces had been cultivated by indigenous peoples in the mountainous regions with an upland practice. A total of 60 upland rice accessions were collected from the indigenous villages from 1895 to the early 1900s. These accessions were since propagated (renewed) about every 10 years by rice breeders, and seeds were stored in NPGRC, TARI. There are only names for this seed resource, without other information such as collecting time, villages and tribes. Some rice breeders visited mountain regions and collected more accessions in recent years and added another approximately 70 lines, with information on tribes collected. These accessions are highly diverse in seed morphology, plant height, plant stature, heading behavior, etc., as shown in our previous studies (Hsieh \u003cem\u003eet al.\u003c/em\u003e 2011; Sagart \u003cem\u003eet al.\u003c/em\u003e 2018; Wu \u003cem\u003eet al.\u003c/em\u003e 2020a).\u003c/p\u003e \u003cp\u003eThe Han people migrated to Taiwan from the southeast coastal area in China, mainly Fujian and Guangdong, to Taiwan during the late Ming to early Ching Dynasty about 400 years ago. The rice accessions they brought were designated \u0026ldquo;Ming-Ching\u0026rdquo; in the current study. According to the literature, there were 1,679 Ming-Ching accessions during the survey in 1906, and the breeders reduced these to 547 lines after screening and elimination according to similarity in morphology (Iso 1944). All these resources were also stored in NPGRC. We chose 58 accessions from this collection for the current analysis. These accessions represented the old landraces in southern China about 400 years ago.\u003c/p\u003e \u003cp\u003eModern breeding programs have been applied for improving rice varieties, including \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e, in Taiwan since the 1920s. Both breeding lines (the intermediate lines during the breeding process for new varieties) and modern varieties (finished the complete breeding process and were assigned names) were chosen for this study; they belong to the category \u0026ldquo;modern\u0026rdquo; rice. Red rice, also known as weedy rice, has been a problem in rice production practice in Taiwan in recent years (Huang \u003cem\u003eet al.\u003c/em\u003e 2021; Wu \u003cem\u003eet al.\u003c/em\u003e 2020b). One red rice accession was also used for the present analysis. A wild rice (\u003cem\u003eOryza rufipogon\u003c/em\u003e) population existed in northern Taiwan previously and had become extinct on the site around 1978 (Kiang 1979). Some of these accessions were kept by rice breeders in the Miaoli Agriculture Research Station, and we received 2 lines for the current study.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec12\" class=\"Section2\"\u003e \u003ch2\u003eClassification of the indigenous upland rice accessions\u003c/h2\u003e \u003cp\u003eWe prepared a rice genomics and phenomics resource of 500 accessions primarily with Taiwan rice accessions previously described (Wu \u003cem\u003eet al.\u003c/em\u003e 2022). This resource consists of the genome sequencing data for 265 Taiwan accessions along with temperate \u003cem\u003ejaponica\u003c/em\u003e, subtropical \u003cem\u003ejaponica\u003c/em\u003e, tropical \u003cem\u003ejaponica\u003c/em\u003e, \u003cem\u003eindica\u003c/em\u003e, \u003cem\u003eaus\u003c/em\u003e, and \u003cem\u003earomatic\u003c/em\u003e accessions collected from other Asia countries where rice is the major staple food. We used 500 accessions for phylogenetic, structure and genome-wide association analyses. Structure analysis at K\u0026thinsp;=\u0026thinsp;9 (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e, Wu\u003cem\u003eet al.\u003c/em\u003e 2022) could separate the accessions into 9 categories: \u003cem\u003ejaponica\u003c/em\u003e accessions into 4 groups (i.e., V1, V2, V4 and V7), \u003cem\u003eindica\u003c/em\u003e into 4 groups (V3, V5, V6 and V8) and wild rice accessions as V9. The 265 lines in the current study were classified into these 9 groups (Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e), with the detailed information for each accession presented in Table \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab2\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eDetail information of the V1 to V9 groups classified by using structure analysis.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"5\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eGroup\u003c/p\u003e \u003cp\u003e#\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSubtype\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eTotal number\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTaiwan number*\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eDescriptions\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eV1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eTemp \u003cem\u003ejap\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e40\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e40 (40)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eAll accessions were from Taiwan, with primitive traits such as long awn and shattered.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eV2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSubtrop \u003cem\u003ejap\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e35\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e17 (17)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eMost were from Indochina.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eV3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eIndica\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e48\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e4 (1)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eMost were from Indian Subcontinent.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eTemp \u003cem\u003ejap\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e87\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e73 (18)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eMost were modern varieties from Taiwan and Japan\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eV5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eIndica\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e99\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e9 (2)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eMost were from Indochina and insular southeast Asia.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eV6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eIndica\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e55\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e44 (5)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eMost were from indigenous and Mingching of Taiwan\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eV7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eTrop \u003cem\u003ejap\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e72\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e16 (12)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eMost were from insular southeast Asia.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eV8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eIndica\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e65\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e61 (34)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eMost were from indigenous and Mingching of Taiwan\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eV9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eWild rice\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e14\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eWild rice collected in Asia\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003e*Accessions numbers collected from Taiwan, with the indigenous ones in brackets.\u003c/p\u003e \u003cp\u003eTo summarize: the indigenous temperate \u003cem\u003ejaponica\u003c/em\u003e accessions were grouped into V1 and V4, with the primitive types in V1 and modern ones in V4. For the follow-up analysis, V1 and V4 were assayed differently. Indigenous rice accessions in V2 were subtropical \u003cem\u003ejaponica\u003c/em\u003e and in V7 tropical \u003cem\u003ejaponica\u003c/em\u003e. For the \u003cem\u003eindica\u003c/em\u003e rice, those in V3 were classified with accessions from the Indian subcontinent and V5 with accessions from the mainland- and insular-SEA. It is intriguing to note that those in V6 and V8 were grouped with Taiwan landraces themselves.\u003c/p\u003e \u003cp\u003eWe used several early primitive traits such as long awn and red caryopsis to postulate which subtype of rice arrived Taiwan at an early time, that is, indigenous accessions. Table\u0026nbsp;\u003cspan refid=\"Tab3\" class=\"InternalRef\"\u003e3\u003c/span\u003e lists the accessions numbers and percentage of these traits. In the indigenous temperate \u003cem\u003ejaponica\u003c/em\u003e, 4- or 5-fold more accessions have long awns and red caryopsis in V1 versus V4. About half of the indigenous subtropical \u003cem\u003ejaponica\u003c/em\u003e accessions contained long awns, with none in the tropical \u003cem\u003ejaponica\u003c/em\u003e lines. In all, 5.9% and 16.7% of the subtropical and tropical \u003cem\u003ejaponica\u003c/em\u003e accessions had a red caryopsis. Because \u003cem\u003eindica\u003c/em\u003e rice arrived from EA and SEA relatively late (Castillo \u003cem\u003eet al.\u003c/em\u003e 2016), the early cultivated rice in Taiwan must be the \u003cem\u003ejaponica\u003c/em\u003e type. From the phenotype of indigenous rice lines, the temperate lines may have arrived the earliest, followed by the subtropical and then tropical lines. However, \u003cem\u003eindica\u003c/em\u003e indeed arrived quite late because only 5.1% had long awns. About half (46.2%) of the indigenous \u003cem\u003eindica\u003c/em\u003e rice accessions had a red caryopsis, probably because the early \u003cem\u003eindica\u003c/em\u003e in nearby regions was still colored rice during that time.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab3\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 3\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003ePhenotyping information of grain-related traits in Taiwan indigenous rice accessions.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"4\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLong awn\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eRed caryopsis\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eGlutenous endosperm\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colspan=\"4\" nameend=\"c4\" namest=\"c1\"\u003e \u003cp\u003eIndigenous\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTemperate \u003cem\u003ejap\u003c/em\u003e (V1)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e23/40\u0026thinsp;=\u0026thinsp;57.5%\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e19/40\u0026thinsp;=\u0026thinsp;47.5%\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e36/40\u0026thinsp;=\u0026thinsp;90%\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTemperate \u003cem\u003ejap\u003c/em\u003e (V4)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e2/18\u0026thinsp;=\u0026thinsp;11.1%\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e2/18\u0026thinsp;=\u0026thinsp;11.1%\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e3/18\u0026thinsp;=\u0026thinsp;16.7%\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSubtropical \u003cem\u003ejap\u003c/em\u003e (V2)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e9/17\u0026thinsp;=\u0026thinsp;52.9%\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1/17\u0026thinsp;=\u0026thinsp;5.9%\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e5/17\u0026thinsp;=\u0026thinsp;29.4%\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTropical \u003cem\u003ejap\u003c/em\u003e (V7)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0/12\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e2/12\u0026thinsp;=\u0026thinsp;16.7%\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e5/12\u0026thinsp;=\u0026thinsp;41.7%\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eIndica\u003c/em\u003e (V3\u0026thinsp;+\u0026thinsp;V5\u0026thinsp;+\u0026thinsp;V6\u0026thinsp;+\u0026thinsp;V8)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e2/39\u0026thinsp;=\u0026thinsp;5.1%\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e18/39\u0026thinsp;=\u0026thinsp;46.2%\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e13/39\u0026thinsp;=\u0026thinsp;33.3%\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eAdmixture\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0/3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1/3\u0026thinsp;=\u0026thinsp;33%\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0/3\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colspan=\"4\" nameend=\"c4\" namest=\"c1\"\u003e \u003cp\u003eMingching\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eIndica\u003c/em\u003e (V3\u0026thinsp;+\u0026thinsp;V5\u0026thinsp;+\u0026thinsp;V6\u0026thinsp;+\u0026thinsp;V8)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0/58\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e6/58\u0026thinsp;=\u0026thinsp;10.3%\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e4/58\u0026thinsp;=\u0026thinsp;6.9%\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colspan=\"4\" nameend=\"c4\" namest=\"c1\"\u003e \u003cp\u003eModern\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eAdmixture\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0/1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0/1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0/1\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTropical \u003cem\u003ejap\u003c/em\u003e (V7)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0/4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0/4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0/4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTemperate \u003cem\u003ejap\u003c/em\u003e (V4)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0/54\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0/54\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e3/54\u0026thinsp;=\u0026thinsp;5.6%\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eIndica\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0/16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0/16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e5/16\u0026thinsp;=\u0026thinsp;31%\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colspan=\"4\" nameend=\"c4\" namest=\"c1\"\u003e \u003cp\u003eRed rice (weedy)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eIndica\u003c/em\u003e (V6)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0/1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1/1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0/1\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003eGlutinous rice has been important in indigenous villages because it is used to make wine and rice pudding. The wine is important for sacrifice ceremonies as well as at entertainment parties. Thus, we checked the sticky grains: 90%, 16.7%, 29.4%, 41.7% and 33.3% accessions are the glutinous type for temperate V1, temperate V4, subtropical V2, tropical V7 \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e rice, respectively. For comparison, Ming-Ching and modern rice each have much less sticky rice (about or \u0026lt;\u0026thinsp;10%). Thus, glutinous rice is specifically popular in the indigenous accessions.\u003c/p\u003e \u003cp\u003e \u003cb\u003eOnly\u003c/b\u003e \u003cb\u003eindica\u003c/b\u003e \u003cb\u003elandraces were cultivated in the plain region since the Han people arrived in the early 17th century\u003c/b\u003e \u003c/p\u003e \u003cp\u003eThe Han people had been living in the plain region since their arrival and most indigenous villages were moved to high mountain regions. All rice accessions grown in the plain region since then were \u003cem\u003eindica\u003c/em\u003e rice according to the history book related to Taiwan rice cultivation (DAFTPG 1989; Teng 2003) and sequencing information (Wu \u003cem\u003eet al.\u003c/em\u003e 2022), so most, if not all, landraces cultivated in southern China must have been \u003cem\u003eindica\u003c/em\u003e rice during the late Ming Dynasty. In a survey of rice accessions preserved by TARI (searchable at the NPGRC website, \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.npgrc.tari.gov.tw/npgrc1/index_e.html\u003c/span\u003e\u003cspan address=\"https://www.npgrc.tari.gov.tw/npgrc1/index_e.html\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e), 54 of 450 of these Ming-Ching lines are glutinous and all others are wild type. In addition, 19 of the 450 lines have a red caryopsis and all others are white, and 2 of these lines have long awns. As compared with the indigenous rice accessions, no or only a small proportion of the rice grains of these lines have long awns or red caryopsis.\u003c/p\u003e \u003cp\u003eOne of the most important traits for the Ming-Ching accessions was semidwarf (sd). This trait was used in the breeding of IR8, the miracle rice, and played important roles in \u003cem\u003eindica\u003c/em\u003e rice breeding worldwide since the 1960s (Khush 1995, 1999). This trait came from the Dee-Geo-Woo-Gen (DGWG) \u003cem\u003esd1\u003c/em\u003e allele, one of the Ming-Ching accessions. The mutation was caused by a 383-bp deletion in the gene \u003cem\u003eGA\u003c/em\u003e\u003csub\u003e\u003cem\u003e20\u003c/em\u003e\u003c/sub\u003e\u003cem\u003eoxidase-2\u003c/em\u003e (Os01t0883800) (Sasaki \u003cem\u003eet al.\u003c/em\u003e 2002), which led to the abolishment of this GA\u003csub\u003e20\u003c/sub\u003e oxidase function. We checked all Ming-Ching accessions and found that in addition to DGWG, another 4 accessions also contained the \u003cem\u003esd1-DGWG\u003c/em\u003e allele: Hsinchu-Ai-Chueh-Chien, Ti-Chueh-Wu-Ko, Ai-Tzu-Chung, and Liu-Tou-Tzu.\u003c/p\u003e \u003cp\u003e \u003cb\u003eMajor modern rice accessions were\u003c/b\u003e \u003cb\u003ejaponica\u003c/b\u003e \u003cb\u003erice due to the taste preference during Japanese colonial times\u003c/b\u003e \u003c/p\u003e \u003cp\u003eDuring the Japanese colonial period (1895 to 1945), Taiwan rice cultivation had gradually shifted to temperate \u003cem\u003ejaponica\u003c/em\u003e accessions. According to several reviews, including DAFTPG (1989) and Teng (2003), this huge change was due to the taste preference of Japanese people. All the cultivated accessions in the plain region before 1920 were \u003cem\u003eindica\u003c/em\u003e type and there were few \u003cem\u003ejaponica\u003c/em\u003e types since 1925, with the percentage of \u003cem\u003eindica\u003c/em\u003e and \u003cem\u003ejaponica\u003c/em\u003e being 87.5% and 12.5%, respectively. The earliest \u003cem\u003ejaponica\u003c/em\u003e variety was Taichung 65, which was designated in 1929 (Iso 1944; Wei \u003cem\u003eet al.\u003c/em\u003e 2016b). The percentage of \u003cem\u003eindica\u003c/em\u003e type then gradually decreased to 32.9% in 1944. There was a small increase during 1945 and 1946, with the ratio being 47.1% and 65.4%, respectively. The \u003cem\u003eindica\u003c/em\u003e rice proportion then gradually decreased again (Teng 2003) and has been less than 10% in the recent decade (data from the Council of Agriculture, Taiwan). By using the sequencing information for new accessions since breeding was applied to rice cultivation, only 4 and 12 breeding lines and new varieties, respectively, for \u003cem\u003eindica\u003c/em\u003e rice, versus 13 and 46, respectively, for \u003cem\u003ejaponica\u003c/em\u003e rice (Table \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e). Thus, \u003cem\u003ejaponica\u003c/em\u003e varieties gained more attention in the breeding programs.\u003c/p\u003e \u003cp\u003eThe \u003cem\u003esd1\u003c/em\u003e trait has been used in more than 90% of the modern rice varieties worldwide. This \u003cem\u003eDGWG\u003c/em\u003e 383-bp deletion was present in all Taiwan modern \u003cem\u003eindica\u003c/em\u003e varieties as well as the weedy rice tested. We also checked its presence in the modern \u003cem\u003ejaponica\u003c/em\u003e varieties. Taikeng 9 had an \u003cem\u003eindica\u003c/em\u003e type (IR5470) as one of its parental lines; however, sequence analysis revealed that it did not contain this mutation in the \u003cem\u003eSD1\u003c/em\u003e locus. The same is true for all other \u003cem\u003ejaponica\u003c/em\u003e varieties without \u003cem\u003eindica\u003c/em\u003e rice in their pedigree. Thus, even though the \u003cem\u003eDGWG sd1\u003c/em\u003e allele has been used in most \u003cem\u003eindica\u003c/em\u003e and some \u003cem\u003ejaponica\u003c/em\u003e varieties worldwide, it was not present in any modern Taiwanese \u003cem\u003ejaponica\u003c/em\u003e variety.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec13\" class=\"Section2\"\u003e \u003ch2\u003eChanges in phenotypes related to stress tolerance\u003c/h2\u003e \u003cp\u003ePreviously, we established a resource for rice genome-wide association study with about 500 accessions of selected upland rice and landraces from Taiwan and Asia, along with some modern varieties (Wu \u003cem\u003eet al.\u003c/em\u003e 2022). We performed phenotyping studies of seedlings including study of resistance to flooding, drought and abscisic acid (ABA) treatments. Together, information for 19 phenotypes was obtained, including 1) drought survival rate after 25% PEG treatment (severe osmotic stress), 2) ratio of shoot length after flooding treatment for 7 days (compared with control), 3) ratio of root length after flooding treatment for 7 days (compared with control), 4) ratio of total root length after 0.5 \u0026micro;M ABA treatment (compared with control), 5) ratio of crown root length after 0.5 \u0026micro;M ABA treatment (compared with control), 6) ratio of primary root length after 0.5 \u0026micro;M ABA treatment (compared with control), 7) ratio of crown root number after 0.5 \u0026micro;M ABA treatment (compared with control), 8) root length under the control condition, 9) root length after 7 day flooding treatment, 10) shoot length under the control condition, 11) shoot length after 7 day flooding treatment, 12) total root length under the control condition, 13) total root length after 0.5 \u0026micro;M ABA treatment, 14) crown root length under the control condition, 15) crown root length after 0.5 \u0026micro;M ABA treatment, 16) primary root length under the control condition, 17) primary root length after 0.5 \u0026micro;M ABA treatment, 18) crown root number under the control condition, and 19) crown root number after 0.5 \u0026micro;M ABA treatment. Figure\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e illustrates the phenotype histograms for the \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e populations under stress conditions. Panels A and B show the root length response to 7-day flooding treatment, and C and D show the survival rate after 3-day 25% PEG treatment. The red arrows indicate the position of control varieties Tainung 67 (\u003cem\u003ejaponica\u003c/em\u003e) or Taichung Native 1 (\u003cem\u003eindica\u003c/em\u003e). Two kinds of landraces were included: Ming-Ching and indigenous ones. The results of both modern varieties or landraces was normal distribution for most phenotypes checked. For the drought-resistant trait of \u003cem\u003eindica\u003c/em\u003e rice accessions, the distribution was skewed toward more resistance. Even though some landraces showed higher resistance to the stress treatments, some modern varieties also provided similar protection.\u003c/p\u003e \u003cp\u003eSupplementary Fig.\u0026nbsp;1 panels A to AL illustrate the other histograms for the 19 phenotypes. All show a similar trend, that is, normal distribution; some landraces and a few modern varieties feature resistant phenotypes.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec14\" class=\"Section2\"\u003e \u003ch2\u003eChanges in genetic diversity\u003c/h2\u003e \u003cp\u003eWe used phylogenetic, structure and principle component analyses to show the diversity and classification of the 500 accessions (Wu \u003cem\u003eet al.\u003c/em\u003e 2022). The Taiwanese accessions were grouped into 9 sessions with K\u0026thinsp;=\u0026thinsp;9 for the structure analysis, as shown in the classification section.\u003c/p\u003e \u003cp\u003eWe explored the genetic diversity among these groups by checking for the existence of positive selection of 20 domestication- or adaptation-related genes (listed in Table \u003cspan refid=\"MOESM3\" class=\"InternalRef\"\u003eS3\u003c/span\u003e with gene locus information and references). We calculated selection parameters, including \u003cem\u003eπ\u003c/em\u003e (Tajima 1983), \u003cem\u003eθw\u003c/em\u003e (Watterson 1975), as well as Tajima\u0026rsquo;s \u003cem\u003eD\u003c/em\u003e (Tajima 1989), to test the neutral mutation hypothesis. The nearby region (\u0026plusmn;\u0026thinsp;1 Mb) of each gene were used for the calculation and the results are listed in Table\u0026nbsp;\u003cspan refid=\"Tab4\" class=\"InternalRef\"\u003e4\u003c/span\u003e and Table \u003cspan refid=\"MOESM4\" class=\"InternalRef\"\u003eS4\u003c/span\u003e. The genes of a specific group with significant selection are listed and the information illustrated huge differences among each group. For instance, 19 genes were under selection for Taiwanese V4 group, so only \u003cem\u003eTGW6\u003c/em\u003e was not under selection for the modern Taiwan temperate \u003cem\u003ejaponica\u003c/em\u003e rice accessions. For other groups, only a few genes showed significant selection; they are \u003cem\u003eGn1, qSH1\u003c/em\u003e and \u003cem\u003eqSW5\u003c/em\u003e genes for V1; \u003cem\u003eBh4, Lg1, OsC1, Prog1\u003c/em\u003e and \u003cem\u003eTGW6\u003c/em\u003e genes for V2; \u003cem\u003eRAE2\u003c/em\u003e gene for V6; \u003cem\u003eProg1\u003c/em\u003e and \u003cem\u003eqSH1\u003c/em\u003e genes for V7; and \u003cem\u003eAn1, An2, Bh4, Edh1\u003c/em\u003e and \u003cem\u003eWaxy\u003c/em\u003e genes for V8. There was no significant selection for V3 and V5 among the 20 genes tested. Both groups include relatively primitive \u003cem\u003eindica\u003c/em\u003e accessions in Taiwan. Thus, the genetic diversity has changed during cultivation and differs according to population.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab4\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 4\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eSelection swept analysis of some domestication- or adaption-related genes of Taiwan rice accessions. The gene region and the nearby\u0026thinsp;\u0026plusmn;\u0026thinsp;1 Mb were used for the calculation. Only significant traits/groups are listed.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"6\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eGene\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eGroup classification\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNumber of\u003c/p\u003e \u003cp\u003esequences\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eπ\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eθw\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003eTajima's D\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eAn1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.07522\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.20383\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.21879**\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eAn1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e61\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.10125\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.21108\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-1.86562*\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eAn2\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.03095\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.20471\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.98748***\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eAn2\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e61\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.04019\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.21324\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.90897***\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eBh4\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.10986\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.24517\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.39274***\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eBh4\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.04551\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.20470\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.73676***\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eBh4\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e61\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.08955\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.21322\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.07901*\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCold1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.06909\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.20456\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.33085**\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eEhd1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.03862\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.20563\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.85917***\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eEhd1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e61\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.05927\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.21174\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.58027***\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eGn1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e40\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.06544\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.13948\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-1.99547*\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eGn1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.04106\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.20555\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.81393***\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eHd3a\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.05331\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.20573\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.60790***\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eIPA1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.08698\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.20552\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.02404*\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eLg1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.10085\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.23332\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.46130***\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eLg1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.04990\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.20573\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.66412***\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eOsC1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.14947\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.26621\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-1.90065*\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eOsC1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.05047\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.20573\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.65666***\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eOsLg1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.07352\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.20399\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.25074**\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003ePhr1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.09719\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.20335\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-1.83741*\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eProg1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.11562\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.27046\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.48232***\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eProg1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.07806\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.20573\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.17197**\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eProg1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.14808\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.30137\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.23620**\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eqSh1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e40\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.05931\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.23421\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.81371***\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eqSh1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.03236\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.20561\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.96598***\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eqSh1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.15545\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.29526\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.08093*\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eqSW5\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e40\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.10905\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.23309\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.00318*\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eqSW5\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.07536\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.2057\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.23050**\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eRAE2\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.04642\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.20541\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.71068***\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eRAE2\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e44\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.04697\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.16912\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.68728***\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eRc\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.06071\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.20573\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.48110**\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eTGW6\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.15465\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.2954\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.06686*\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eTT1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.03979\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.20409\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.83281***\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eWx\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.03674\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.20573\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-2.89097***\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eWx\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eV8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e61\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0.09809\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.21346\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e-1.93567*\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003e \u003cb\u003eHeading date 1\u003c/b\u003e \u003cb\u003eallele analysis showed that some indigenous rice accessions came from nearby regions\u003c/b\u003e \u003c/p\u003e \u003cp\u003eRice is a short-day plant and was domesticated in China (a temperate zone), then was brought to subtropical and tropical zones with warmer temperature and different photoperiods. The early rice plants that grew in a temperate region fitted the daylength atmosphere very well: they flowered (also known as heading) during early autumn and were ready to be harvested about 40 days later. However, when the plants were brought to the southern region with short daylength, the reduced vegetative growth period before heading would lead to decreased yield. Many reviews provided detailed information on the regulation of rice flowering and production (e.g., Itoh and Izawa 2013; Lee and An 2015; Tsuji \u003cem\u003eet al\u003c/em\u003e. 2013). Mutations leading to the null function of sensitivity-to-photoperiod genes would increase crop yield because rice could grow in 2 or 3 seasons instead of only one each year and also reduce stress damage caused by seasonal typhoons, monsoons or drought. Thus, such a trait could be selected out in subtropical and tropical regions.\u003c/p\u003e \u003cp\u003eCultivated rice varieties and landraces exhibited large variation in flowering time, so rice heading behavior was controlled by quantitative trait loci (QTL). For instance, by using the progeny derived from a single cross between one \u003cem\u003ejaponica\u003c/em\u003e (Nipponbare) and one \u003cem\u003eaus\u003c/em\u003e (Kasalath) line, researchers identified 15 QTL for the \u003cem\u003eHeading date\u003c/em\u003e (\u003cem\u003eHd\u003c/em\u003e) trait (Yano \u003cem\u003eet al.\u003c/em\u003e 2000). \u003cem\u003eHd1\u003c/em\u003e was one of the most important loci to control rice flowering time and was identified as an Arabidopsis \u003cem\u003eCO\u003c/em\u003e ortholog (Yano \u003cem\u003eet al.\u003c/em\u003e 2000). By using the information from many local accessions (Takahashi \u003cem\u003eet al.\u003c/em\u003e 2009) and the rice 3K project information (Wu \u003cem\u003eet al.\u003c/em\u003e 2020a), about 10 \u003cem\u003eHd1\u003c/em\u003e loss-of-function (LOF) alleles were identified (Yano \u003cem\u003eet al.\u003c/em\u003e 2000; Takahashi \u003cem\u003eet al.\u003c/em\u003e 2009; Wu \u003cem\u003eet al.\u003c/em\u003e 2020a). The rice accessions with any of these LOF \u003cem\u003ehd1\u003c/em\u003e alleles would not be sensitive to photoperiod and thus could flower and mature after proper vegetative growth. Many landraces and most modern varieties in subtropical and tropical regions contained these alleles because they could adapt to the environment well and have high yield. Phylogenetic and haplotype network analysis of several of these alleles revealed that type 7 \u003cem\u003ehd1\u003c/em\u003e LOF mutation occurred in \u003cem\u003eindica\u003c/em\u003e rice in insular areas in SEA, followed by introgression and expansion (i.e., brought by human beings) to nearby regions including the Indochina area and Indian subcontinent (Wu \u003cem\u003eet al.\u003c/em\u003e 2020a). With a similar strategy and dataset, the results also suggested that type 13 mutation occurred in \u003cem\u003ejaponica\u003c/em\u003e rice in insular areas in SEA, followed by introgression and expansion of both \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e accessions to nearby regions. In addition, some other \u003cem\u003ehd1\u003c/em\u003e LOF alleles were specific to local regions: type 3 was \u003cem\u003eindica\u003c/em\u003e-specific and mainly from China, and type 19 was \u003cem\u003ejaponica\u003c/em\u003e-specific and mainly from Taiwan (Wu \u003cem\u003eet al.\u003c/em\u003e 2020a).\u003c/p\u003e \u003cp\u003eData mining analysis of the 129 Taiwan indigenous rice accessions in the current study indicated that 6 contained type 13 \u003cem\u003ehd1\u003c/em\u003e alleles, including 5 \u003cem\u003ejaponica\u003c/em\u003e accessions and one \u003cem\u003eindica\u003c/em\u003e. In addition, 5 \u003cem\u003eindica\u003c/em\u003e accessions had type 7 alleles, 14 \u003cem\u003ejaponica\u003c/em\u003e accessions had the type 19 \u003cem\u003ehd1\u003c/em\u003e allele, and 3 \u003cem\u003eindica\u003c/em\u003e accessions had the type 3 allele. Thus, the variations in the \u003cem\u003ehd1\u003c/em\u003e allele type revealed that some of the early rice cultivated in Taiwan came from China and mainland or insular SEA. There must have been intensive exchanges of rice accessions in Taiwan with the nearby regions a long time ago.\u003c/p\u003e \u003c/div\u003e"},{"header":"Discussion","content":"\u003cp\u003eIn the current study, we performed a detailed analysis of the population structure changes in rice in Taiwan over thousands of years. Multidiscipline strategies including archaeological, morphological, genetic and genomic approaches were used. The materials included carbonized seeds excavated from central or southern Taiwan from 5000 years ago and those cultivated in indigenous villages or plain regions recently. We discuss which rice types arrived Taiwan in ancient times, any exchange of rice lines with nearby regions a long time ago, why there were major changes in the rice population in the last century as well as how domestication- and adaptation-related genes changed in different populations. Finally, we showed factors that have shaped the population structure of Taiwan rice accessions over these years.\u003c/p\u003e \u003cdiv id=\"Sec16\" class=\"Section2\"\u003e \u003ch2\u003eTraditional Taiwan cereals were present 5000 years ago\u003c/h2\u003e \u003cp\u003eRice, foxtail millet and proso millet grains were excavated in southern Taiwan around 5000 BP in large quantity (Tsang \u003cem\u003eet al.\u003c/em\u003e 2017). Multidiscipline analyses on indigenous habitat, linguistic divisions, archaeological remains, etc. were applied to search the early origin of Austronesian. Many studies proposed that the Formosan peoples and culture traits came from southern China by using archaeological data (Ferrell 1966; Bellwood 1997; Chang 1989; Deng \u003cem\u003eet al.\u003c/em\u003e 2022; Tsang 2005) or language (Bellwood 1979; Ferrell 1969).\u003c/p\u003e \u003cp\u003eAlternatively, our recent study provided difference hypothesis. We performed a multidisciplinary analysis from the viewpoint of archaeology, linguistics, and genome sequence as well as seed morphology to reveal early agriculture in Taiwan (Sagart \u003cem\u003eet al.\u003c/em\u003e 2018). By using sequence information for several domestication-related genes, we found that the functional nucleotide polymorphisms of indigenous rice lines were the same as modern \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e rice varieties elsewhere in the world. Thus, the early rice that arrived in Taiwan long time ago was already domesticated and was \u003cem\u003ejaponica\u003c/em\u003e (no \u003cem\u003eindica\u003c/em\u003e rice in eastern Asia yet during that period). \u003cem\u003eIndica\u003c/em\u003e rice arrived in Taiwan rather late, with some modern traits. With the botanically informed linguistic fieldwork of the agricultural vocabulary of indigenous villages, along with the earlier findings in archaeology, genetics and historical linguistics, early Taiwan agriculture was found to be based on foxtail millet, broomcorn millet and rice (Hsieh \u003cem\u003eet al.\u003c/em\u003e 2011; Tsang \u003cem\u003eet al.\u003c/em\u003e 2017). Together, we proposed the pre-Austronesians expanded south along the coast from Northern China 5000 BCE to reach northwest Taiwan in the second half of the 4th millennium BP (Sagart \u003cem\u003eet al.\u003c/em\u003e 2018).\u003c/p\u003e \u003cp\u003eThe archaeological studies indicated that there were continuous rice cultivations in Taiwan from about 5000 years ago to the present time. By using 100 carbonized rice seeds excavated from 4 different sites with a time span from 5000 to 500 BP in southern Taiwan and 1300 BP in central Taiwan, we showed that rice seed size had changed over thousands of years, from a relatively small and round shape to a large and oblonga shape (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Previously we described the seed length, width and grain length/width (l/w) ratio of carbonized rice grains excavated from 18 sites in southern Taiwan (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e, Hsu \u003cem\u003eet al\u003c/em\u003e 2019. The time span ranged from 5000 BP to 300 BP, and the seed size also showed a huge change during the ~\u0026thinsp;5000 years: seed length average 4.72 mm, width 2.52, and l/w ratio 1.88. This analysis again demonstrated that the seeds were small and round before 3000 BP and then became large and long later on. By using the excavated rice seed morphology, there must have been movement of rice between Taiwan and the nearby regions for thousands of years. Using the seed size information, the large seeds might be from SEA, such as Funan, Langkasuka, Salakanagara, Tarumanagara or Champa during that time.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec17\" class=\"Section2\"\u003e \u003ch2\u003eStudies of excavated rice grain indicated the changes in early cultivated rice of Taiwan\u003c/h2\u003e \u003cp\u003eIn the current study, we measured the grain size of hundreds of carbonized rice seeds excavated from 4 sites in central or southern Taiwan (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e, Table \u003cspan refid=\"MOESM5\" class=\"InternalRef\"\u003eS5\u003c/span\u003e). Most rice grains recovered from excavated sites worldwide were preserved by carbonization, a process in which the organic structure was converted into inorganic carbon by heating (Wright 2003). The high temperature could lead to warping, shrinking or fracturing, although the seeds would not be destroyed by microbe decay (Wright 2003). This carbonization process could affect the length and width of rice grains (Ahn 1993). To differentiate \u003cem\u003ejaponica\u003c/em\u003e or \u003cem\u003eindica\u003c/em\u003e carbonized rice seeds, the l/w ratio was used in most studies. Some researchers assume a uniform 20% shrinkage rate for the l/w ratio in the studies of all archaeological carbonized seeds (e.g., Fuller \u003cem\u003eet al\u003c/em\u003e 2008; Fuller \u003cem\u003eet al\u003c/em\u003e 2009; Harvey 2007.\u003c/p\u003e \u003cp\u003eTable \u003cspan refid=\"MOESM5\" class=\"InternalRef\"\u003eS5\u003c/span\u003e illustrates the average, minimum and maximum values of seed length, width and l/w values for NKLE, YHF, WCT and HLL. Using the 20% shrinkage rate, the mean l/w values were 1.98, 2.29, 2.57, and 2.70 for the 4 sites. Information on many agronomic traits, including seed length and width, from the 3K rice project is available from the Rice SNP-Seek website of IRRI (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://snp-seek.irri.org/\u003c/span\u003e\u003cspan address=\"https://snp-seek.irri.org/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e). Using the traditional accessions (1048 lines) only, the l/w ratios were 3.05, 2.61, 3.31, 2.80, 3.06, 2.90, 2.17, 2.64 and 2.64 for \u003cem\u003earomatic\u003c/em\u003e, \u003cem\u003eaus\u003c/em\u003e, \u003cem\u003eind\u003c/em\u003e1A, \u003cem\u003eind\u003c/em\u003e1B, \u003cem\u003eind\u003c/em\u003e2, \u003cem\u003eind\u003c/em\u003e3, temperate \u003cem\u003ejaponica\u003c/em\u003e, tropical \u003cem\u003ejaponica\u003c/em\u003e and subtropical \u003cem\u003ejaponica\u003c/em\u003e, respectively. Thus, the very early rice lines that may have been cultivated in Taiwan before 3800 BP (NKLE and YHF) were temperate \u003cem\u003ejaponica\u003c/em\u003e type. Since about 1500 BP (WCT and HLL), there were subtropical and tropical \u003cem\u003ejaponica\u003c/em\u003e as well as \u003cem\u003eindica\u003c/em\u003e rice types according to the higher l/w values. This hypothesis coincided with the classification of the indigenous upland rice accessions: some primitive temperate \u003cem\u003ejaponica\u003c/em\u003e (V1 group) belong to the earliest type that arrived in Taiwan a long time ago.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec18\" class=\"Section2\"\u003e \u003ch2\u003eComplicated exchange with nearby regions before the late Ming Dynasty\u003c/h2\u003e \u003cp\u003eMany ornaments and tools excavated from eastern Taiwan since ~\u0026thinsp;3000 BP were made of Fengtian jade (Hung \u003cem\u003eet al.\u003c/em\u003e 2007). More than 100 sites dating from the early Neolithic to the Iron Age revealed an intensive jade production/industry in eastern Taiwan during that period. Electron probe microanalysis revealed that Fengtian jade was also present in excavated sites in the Philippines, Indonesia, Vietnam, Cambodia, Thailand, Malaysia and southern China (Hung \u003cem\u003eet al.\u003c/em\u003e 2007; Hung \u003cem\u003eet al.\u003c/em\u003e 2013; Alam \u003cem\u003eet al.\u003c/em\u003e 2021). Therefore, there was frequent cultural contact between Taiwan and the insular areas as well as mainland SEA. With the extensive sea-based trade networks in the prehistoric world, rice seeds would accompany other crops.\u003c/p\u003e \u003cp\u003eThe route of early \u003cem\u003ejaponica\u003c/em\u003e rice dispersal to Taiwan, the Philippines and other SEA areas was reconstructed using the whole-genome resequencing of landraces (Alam \u003cem\u003eet al.\u003c/em\u003e 2021). The \u003cem\u003ejaponica\u003c/em\u003e component of the Taiwanese indigenous rice accessions consisted of two distinct populations, including a result of admixture between temperate \u003cem\u003ejaponica\u003c/em\u003e that presumably came from northeast Asia and tropical \u003cem\u003ejaponica\u003c/em\u003e from the northern Philippines and mainland SEA (Alam et al 2021). In the current study, we also illustrated that some indigenous rice lines with different \u003cem\u003ehd1\u003c/em\u003e LOF alleles were brought to Taiwan from mainland and insular SEA as well as China during the early time. Thus, there was a complicated exchange in Taiwan rice accessions with nearby regions before the late Ming Dynasty (arrival of the Han people).\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec19\" class=\"Section2\"\u003e \u003ch2\u003eRice landraces in Taiwan provide good genetic resources for future breeding\u003c/h2\u003e \u003cp\u003eIn the current study, some of the Taiwan rice landraces, including indigenous and Ming-Ching ones, are highly resistant to abiotic stresses such as drought or flooding (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e and Figure \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e), specifically the indigenous rice accessions that were cultivated in an upland practice at higher altitudes for thousands of years. In a genome-wide study of Asian \u003cem\u003ejaponica\u003c/em\u003e landraces, several selection sweeps occurred across 12 chromosomes. The one in the long arm of chromosome 1 was due to some Taiwan indigenous rice lines, and the peak coincided with genes associated with UV tolerance (Alam \u003cem\u003eet al.\u003c/em\u003e 2021). Therefore, these lines were resistant to several stress treatments, and they all contained good traits ready for breeding.\u003c/p\u003e \u003cp\u003eClimate change in recent years has caused serious problems worldwide, including to agricultural production. Problems include flooding, drought, heat, chilling, high UV, etc. Taiwanese indigenous peoples and traditional farmers have kept the rice landraces for hundreds and up to thousands of years. With many old traits preserved, they are good resources for future breeding programs.\u003c/p\u003e \u003c/div\u003e"},{"header":"Abbreviations","content":"\u003cp\u003eNan-kuan-li East, NKLE; Youhsienfang, YHF; Wuchiantsuo, WCT; Huilaili, HLL; Taiwan Agricultural Research Institute, TARI; National Plant Genetic Resources Center, NPGRC; southeast Asia, SEA; Dee Geo Woo Gen, DGWG\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgements\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe would like to acknowledge our gratitude to the Taiwanese indigenous peoples and traditional farmers for their stewardship of traditional rice landraces. We thank Ms. Lie-Hong Wu for maintaining greenhouse plants. We also thank Laura Smales (BioMedEditing, Toronto, Canada) for English editing.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis work was supported by the MOST grants 110-2313-B-001-005 and 109-2313-B-001-008 to YIH as well as ITAR grants AS-ITAR-110-TD06, AS-109-ITAR-TD08 and AS-108-ITAR-TD08 to THDH, SMY and YIH.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData Availability\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe data underlying this article are available in the NCBI Short Read Archive (SRA) database (project accessions nos. PRJNA485658, PRJNA373799, PRJNA623980, and PRJEB6180).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthors\u0026rsquo; contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eYICH conceived and designed the study, CCW, CKL and LTH generated sequencing data. YHW, YCT, TFH and YTT analyzed the carbonized grains. YCT, NCD, JCL, DPS, CWW, MHL, DHW, SC, YPW and SJC collected rice accessions. CCW, CKL, FJW performed bioinformatics analysis. CHT, KTL, WLC provided archaeological materials. THDH, SMY and LS participated in frequent discussions. YICH wrote the manuscript with input from all authors.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n \u003cli\u003e3KRGP (2014) The 3,000 Rice Genomes Project. \u003cstrong\u003eGigaScience\u003c/strong\u003e 3 (1):2047-2217X-2043-2047\u003c/li\u003e\n \u003cli\u003eAhn S-M (1993) Origin and Differentiation of Domesticated Rice in Asia-Review of Archaeological and Botanical Evidences. University of London, University College London (United Kingdom),\u003c/li\u003e\n \u003cli\u003eAlam O, R M Gutaker, C-C Wu, K A Hicks, K Bocinsky, C C Castillo, S Acabado, D Fuller, J A d\u0026rsquo;Alpoim Guedes, Y-I Hsing, M D Purugganan (2021) Genome Analysis Traces Regional Dispersal of Rice in Taiwan and Southeast Asia. \u003cstrong\u003eMolecular Biology and Evolution\u003c/strong\u003e 38 (11):4832-4846. doi:10.1093/molbev/msab209\u003c/li\u003e\n \u003cli\u003eAshikari M, H Sakakibara, S Lin, T Yamamoto, T Takashi, A Nishimura, E R Angeles, Q Qian, H Kitano, M Matsuoka (2005) Cytokinin Oxidase Regulates Rice Grain Production. \u003cstrong\u003eScience\u003c/strong\u003e 309 (5735):741-745. doi:10.1126/science.1113373\u003c/li\u003e\n \u003cli\u003eBellimod P (2004) The Origins and Dispersals of Agricultural Communities in Southeast Asia. \u003cstrong\u003eSoutheast Asia: from prehistory to history\u003c/strong\u003e:21-40\u003c/li\u003e\n \u003cli\u003eBellwood P (1979) Man\u0026apos;s Conquest of the Pacific: The Prehistory of Southeast Asia and Oceania. New York: Oxford Univ. Press.\u0026middot; 1985. Prehistory of the Indo-Malaysianarchipelago. New York: Academic Press,\u003c/li\u003e\n \u003cli\u003eBellwood P (1997) Prehistory of the Indo-Malaysian Archipelago. Honolulu. \u003cstrong\u003eUniversity of Hawaii Press(First edition published 1985 by Academic Press, Sydney) INDO-PACIFIC PREHISTORY ASSOCIATION BULLETIN\u003c/strong\u003e 23:2003\u003c/li\u003e\n \u003cli\u003eBellwood P (2023) First Farmers: The Origins of Agricultural Societies. John Wiley \u0026amp; Sons,\u003c/li\u003e\n \u003cli\u003eBessho-Uehara K, D R Wang, T Furuta, A Minami, K Nagai, R Gamuyao, K Asano, R B Angeles-Shim, Y Shimizu, M Ayano, N Komeda, K Doi, K Miura, Y Toda, T Kinoshita, S Okuda, T Higashiyama, M Nomoto, Y Tada, H Shinohara, Y Matsubayashi, A Greenberg, J Wu, H Yasui, A Yoshimura, H Mori, S R McCouch, M Ashikari (2016) Loss of Function at Rae2, a Previously Unidentified Epfl, Is Required for Awnlessness in Cultivated Asian Rice. \u003cstrong\u003eProc Natl Acad Sci U S A\u003c/strong\u003e 113 (32):8969-8974. doi:10.1073/pnas.1604849113\u003c/li\u003e\n \u003cli\u003eBlust R (1995) The Prehistory of the Austronesian-Speaking Peoples: A View from Language. \u003cstrong\u003eJournal of World prehistory\u003c/strong\u003e 9 (4):453-510\u003c/li\u003e\n \u003cli\u003eCastillo C C, K Tanaka, Y-I Sato, R Ishikawa, B Bellina, C Higham, N Chang, R Mohanty, M Kajale, D Q Fuller (2016) Archaeogenetic Study of Prehistoric Rice Remains from Thailand and India: Evidence of Early Japonica in South and Southeast Asia. \u003cstrong\u003eArchaeological and Anthropological Sciences\u003c/strong\u003e 8 (3):523-543. doi:10.1007/s12520-015-0236-5\u003c/li\u003e\n \u003cli\u003eChang K-c (1989) Taiwan Archaeology in Pacific Perspective. In Chang, K. C., Li, K. C., Wolf, A. P., and Yin, A. C. (Eds.). \u003cstrong\u003eAnthropological Studies of the Taiwan Area: Accomplishments and Prospects, Taipei: Department of Anthropology, National Taiwan University\u003c/strong\u003e:87-97\u003c/li\u003e\n \u003cli\u003eChu W L (2016) Rescue Excavation Report of the Anhelu Site. \u003cstrong\u003eTaichung: National Museum of Natural Science (in Chinese)\u003c/strong\u003e\u003c/li\u003e\n \u003cli\u003eDAFTPG (1989) The History of Taiwan Rice Development and Production. \u003cstrong\u003eDepartment of Agriculture and Forestry of the Taiwan Provincial Government (DAFTPG) (in Chinese)\u003c/strong\u003e:837\u003c/li\u003e\n \u003cli\u003eDanecek P, A Auton, G Abecasis, C A Albers, E Banks, M A DePristo, R E Handsaker, G Lunter, G T Marth, S T Sherry (2011) The Variant Call Format and Vcftools. \u003cstrong\u003eBioinformatics\u003c/strong\u003e 27 (15):2156-2158\u003c/li\u003e\n \u003cli\u003eDeng Z, S-c Kuo, M T Carson, H-c Hung (2022) Early Austronesians Cultivated Rice and Millet Together: Tracing Taiwan\u0026apos;s First Neolithic Crops. \u003cstrong\u003eFrontiers in Plant Science\u003c/strong\u003e:2393\u003c/li\u003e\n \u003cli\u003eDeng Z, L Qin, Y Gao, A R Weisskopf, C Zhang, D Q Fuller (2015) From Early Domesticated Rice of the Middle Yangtze Basin to Millet, Rice and Wheat Agriculture: Archaeobotanical Macro-Remains from Baligang, Nanyang Basin, Central China (6700\u0026ndash;500 Bc). \u003cstrong\u003ePLoS One\u003c/strong\u003e 10 (10):e0139885\u003c/li\u003e\n \u003cli\u003eDoi K, T Izawa, T Fuse, U Yamanouchi, T Kubo, Z Shimatani, M Yano, A Yoshimura (2004) Ehd1, a B-Type Response Regulator in Rice, Confers Short-Day Promotion of Flowering and Controls Ft-Like Gene Expression Independently of Hd1. \u003cstrong\u003eGenes Dev\u003c/strong\u003e 18 (8):926-936. doi:10.1101/gad.1189604\u003c/li\u003e\n \u003cli\u003eEdgar R C (2004a) Muscle: A Multiple Sequence Alignment Method with Reduced Time and Space Complexity. \u003cstrong\u003eBMC Bioinformatics\u003c/strong\u003e 5 (1):113\u003c/li\u003e\n \u003cli\u003eEdgar R C (2004b) Muscle: Multiple Sequence Alignment with High Accuracy and High Throughput. \u003cstrong\u003eNucleic acids research\u003c/strong\u003e 32 (5):1792-1797\u003c/li\u003e\n \u003cli\u003eFerrell R (1966) The Formosan Tribes, a Preliminary Linguistic Archaeological and Cultural Synthesis. na,\u003c/li\u003e\n \u003cli\u003eFerrell R (1969) Taiwan Aboriginal Groups: Problems in Cultural and Linguistic Classification. Institute of Ethnology. \u003cstrong\u003eAcademia Sinica Monograph\u003c/strong\u003e 17\u003c/li\u003e\n \u003cli\u003eFuller D, L Qin, E Harvey (2009) An Evolutionary Model for Chinese Rice Domestication: Reassessing the Data of the Lower Yangtze Region. \u003cstrong\u003eNew Approaches to Prehist Agric\u003c/strong\u003e:312-345\u003c/li\u003e\n \u003cli\u003eFuller D Q, L Qin, E Harvey (2008) A Critical Assessment of Early Agriculture in East Asia, with Emphasis on Lower Yangzte Rice Domestication. \u003cstrong\u003ePragdhara\u003c/strong\u003e 18:17-52\u003c/li\u003e\n \u003cli\u003eFuller D Q, Y-I Sato, C Castillo, L Qin, A R Weisskopf, E J Kingwell-Banham, J Song, S-M Ahn, J Van Etten (2010) Consilience of Genetics and Archaeobotany in the Entangled History of Rice. \u003cstrong\u003eArchaeological and Anthropological Sciences\u003c/strong\u003e 2 (2):115-131\u003c/li\u003e\n \u003cli\u003eGarris A J, T H Tai, J Coburn, S Kresovich, S McCouch (2005) Genetic Structure and Diversity in Oryza Sativa L. \u003cstrong\u003eGenetics\u003c/strong\u003e 169 (3):1631-1638. doi:10.1534/genetics.104.035642\u003c/li\u003e\n \u003cli\u003eGu B, T Zhou, J Luo, H Liu, Y Wang, Y Shangguan, J Zhu, Y Li, T Sang, Z Wang, B Han (2015) An-2 Encodes a Cytokinin Synthesis Enzyme That Regulates Awn Length and Grain Production in Rice. \u003cstrong\u003eMol Plant\u003c/strong\u003e 8 (11):1635-1650. doi:10.1016/j.molp.2015.08.001\u003c/li\u003e\n \u003cli\u003eHarvey E L (2007) Early Agricultural Communities in Northern and Eastern India: An Archaeobotanical Investigation. University of London, University College London (United Kingdom),\u003c/li\u003e\n \u003cli\u003eHill C, P Soares, M Mormina, V Macaulay, D Clarke, P B Blumbach, M Vizuete-Forster, P Forster, D Bulbeck, S Oppenheimer (2007) A Mitochondrial Stratigraphy for Island Southeast Asia. \u003cstrong\u003eThe American Journal of Human Genetics\u003c/strong\u003e 80 (1):29-43\u003c/li\u003e\n \u003cli\u003eHsieh J-s, Y-i C Hsing, T-f Hsu, P J-k Li, K-t Li, C-h Tsang (2011) Studies on Ancient Rice\u0026mdash;Where Botanists, Agronomists, Archeologists, Linguists, and Ethnologists Meet. \u003cstrong\u003eRice\u003c/strong\u003e 4 (3-4):178-183. doi:10.1007/s12284-011-9075-x\u003c/li\u003e\n \u003cli\u003eHsu T, Y Wang, B Fang, Y Chen, Y Tsai, Z Xie, Y-I Hsing (2019) A Comparative Study Onmorphological Types of Carbonized Rice Grains in Prehistorical Taiwan. (Chinese with English Abstract). \u003cstrong\u003eField Archaeology of Taiwan\u003c/strong\u003e 19:55-86\u003c/li\u003e\n \u003cli\u003eHua L, D R Wang, L Tan, Y Fu, F Liu, L Xiao, Z Zhu, Q Fu, X Sun, P Gu, H Cai, S R McCouch, C Sun (2015) Laba1, a Domestication Gene Associated with Long, Barbed Awns in Wild Rice. \u003cstrong\u003ePlant Cell\u003c/strong\u003e 27 (7):1875-1888. doi:10.1105/tpc.15.00260\u003c/li\u003e\n \u003cli\u003eHuang H (1984) Report for the Rescue Excavation of the Chi-Shan-Yen Site. \u003cstrong\u003eTaipei City Archives (in Chinese)\u003c/strong\u003e\u003c/li\u003e\n \u003cli\u003eHuang Y-F, D-H Wu, C-L Wang, P-R Du, C-Y Cheng, C-C Cheng (2021) Survey of Rice Production Practices and Perception of Weedy Red Rice (Oryza Sativa F. Spontanea) in Taiwan. \u003cstrong\u003eWeed Science\u003c/strong\u003e 69 (5):526-535\u003c/li\u003e\n \u003cli\u003eHung H-C, Y Iizuka, P Bellwood, K D Nguyen, B Bellina, P Silapanth, E Dizon, R Santiago, I Datan, J H Manton (2007) Ancient Jades Map 3,000 Years of Prehistoric Exchange in Southeast Asia. \u003cstrong\u003eProceedings of the National Academy of Sciences\u003c/strong\u003e 104 (50):19745-19750\u003c/li\u003e\n \u003cli\u003eHung H-c, K D Nguyen, P Bellwood, M T Carson (2013) Coastal Connectivity: Long-Term Trading Networks across the South China Sea. \u003cstrong\u003eThe Journal of Island and Coastal Archaeology\u003c/strong\u003e 8 (3):384-404\u003c/li\u003e\n \u003cli\u003eIRGSP (2005) The Map-Based Sequence of the Rice Genome. \u003cstrong\u003eNature\u003c/strong\u003e 436 (7052):793-800. doi:10.1038/nature03895\u003c/li\u003e\n \u003cli\u003eIshii T, K Numaguchi, K Miura, K Yoshida, P T Thanh, T M Htun, M Yamasaki, N Komeda, T Matsumoto, R Terauchi, R Ishikawa, M Ashikari (2013) Oslg1 Regulates a Closed Panicle Trait in Domesticated Rice. \u003cstrong\u003eNat Genet\u003c/strong\u003e 45 (4):462-465, 465e461-462. doi:10.1038/ng.2567\u003c/li\u003e\n \u003cli\u003eIshimaru K, N Hirotsu, Y Madoka, N Murakami, N Hara, H Onodera, T Kashiwagi, K Ujiie, B Shimizu, A Onishi, H Miyagawa, E Katoh (2013) Loss of Function of the Iaa-Glucose Hydrolase Gene Tgw6 Enhances Rice Grain Weight and Increases Yield. \u003cstrong\u003eNat Genet\u003c/strong\u003e 45 (6):707-711. doi:10.1038/ng.2612\u003c/li\u003e\n \u003cli\u003eIso E (1944) Lectures on Rice Cultivating in Formosa [Taiwan].\u003c/li\u003e\n \u003cli\u003eItoh H, T Izawa (2013) The Coincidence of Critical Day Length Recognition for Florigen Gene Expression and Floral Transition under Long-Day Conditions in Rice. \u003cstrong\u003eMolecular plant\u003c/strong\u003e 6 (3):635-649\u003c/li\u003e\n \u003cli\u003eJin J, W Huang, J P Gao, J Yang, M Shi, M Z Zhu, D Luo, H X Lin (2008) Genetic Control of Rice Plant Architecture under Domestication. \u003cstrong\u003eNat Genet\u003c/strong\u003e 40 (11):1365-1369. doi:10.1038/ng.247\u003c/li\u003e\n \u003cli\u003eKawahara Y, M de la Bastide, J P Hamilton, H Kanamori, W R McCombie, S Ouyang, D C Schwartz, T Tanaka, J Wu, S Zhou (2013) Improvement of the Oryza Sativa Nipponbare Reference Genome Using Next Generation Sequence and Optical Map Data. \u003cstrong\u003eRice\u003c/strong\u003e 6:1-10\u003c/li\u003e\n \u003cli\u003eKhush G S (1995) Modern Varieties\u0026mdash;Their Real Contribution to Food Supply and Equity. \u003cstrong\u003eGeojournal\u003c/strong\u003e 35 (3):275-284\u003c/li\u003e\n \u003cli\u003eKhush G S (1999) Green Revolution: Preparing for the 21st Century. \u003cstrong\u003eGenome\u003c/strong\u003e 42 (4):646-655\u003c/li\u003e\n \u003cli\u003eKiang Y (1979) The Extinction of Wild Rice (Oryza Perennis Formosana) in Taiwan. \u003cstrong\u003eJ Asian Ecol\u003c/strong\u003e 1:1-9\u003c/li\u003e\n \u003cli\u003eKonishi S, T Izawa, S Y Lin, K Ebana, Y Fukuta, T Sasaki, M Yano (2006) An Snp Caused Loss of Seed Shattering During Rice Domestication. \u003cstrong\u003eScience\u003c/strong\u003e 312 (5778):1392-1396. doi:10.1126/science.1126410\u003c/li\u003e\n \u003cli\u003eLee Y-S, G An (2015) Regulation of Flowering Time in Rice. \u003cstrong\u003eJ Plant Biol\u003c/strong\u003e 58:353-360\u003c/li\u003e\n \u003cli\u003eLi H, B Handsaker, A Wysoker, T Fennell, J Ruan, N Homer, G Marth, G Abecasis, R Durbin (2009) The Sequence Alignment/Map Format and Samtools. \u003cstrong\u003eBioinformatics\u003c/strong\u003e 25 (16):2078-2079\u003c/li\u003e\n \u003cli\u003eLi X-M, D-Y Chao, Y Wu, X Huang, K Chen, L-G Cui, L Su, W-W Ye, H Chen, H-C Chen (2015) Natural Alleles of a Proteasome \u0026Alpha;2 Subunit Gene Contribute to Thermotolerance and Adaptation of African Rice. \u003cstrong\u003eNat Genet\u003c/strong\u003e 47 (7):827-833\u003c/li\u003e\n \u003cli\u003eLiu Y (2011) From Siliao Excavated Site to Niao-Sung Culture Settlement. \u003cstrong\u003eIn: Report for Siliao Archaeological Site Rescue Excavation\u003c/strong\u003e:1-24\u003c/li\u003e\n \u003cli\u003eLu Z, H Yu, G Xiong, J Wang, Y Jiao, G Liu, Y Jing, X Meng, X Hu, Q Qian (2013) Genome-Wide Binding Analysis of the Transcription Activator Ideal Plant Architecture1 Reveals a Complex Network Regulating Rice Plant Architecture. \u003cstrong\u003eThe Plant Cell\u003c/strong\u003e 25 (10):3743-3759\u003c/li\u003e\n \u003cli\u003eLuo J, H Liu, T Zhou, B Gu, X Huang, Y Shangguan, J Zhu, Y Li, Y Zhao, Y Wang, Q Zhao, A Wang, Z Wang, T Sang, Z Wang, B Han (2013) An-1 Encodes a Basic Helix-Loop-Helix Protein That Regulates Awn Development, Grain Size, and Grain Number in Rice. \u003cstrong\u003ePlant Cell\u003c/strong\u003e 25 (9):3360-3376. doi:10.1105/tpc.113.113589\u003c/li\u003e\n \u003cli\u003eMa Y, X Dai, Y Xu, W Luo, X Zheng, D Zeng, Y Pan, X Lin, H Liu, D Zhang, J Xiao, X Guo, S Xu, Y Niu, J Jin, H Zhang, X Xu, L Li, W Wang, Q Qian, S Ge, K Chong (2015) Cold1 Confers Chilling Tolerance in Rice. \u003cstrong\u003eCell\u003c/strong\u003e 160 (6):1209-1221. doi:10.1016/j.cell.2015.01.046\u003c/li\u003e\n \u003cli\u003eMatsuo T, K Hoshikawa (1993) Science of the Rice Plant: Morphology. In, vol 1. Food and Agriculture Policy Research Center, p 686\u003c/li\u003e\n \u003cli\u003eRozas J, A Ferrer-Mata, J C S\u0026aacute;nchez-DelBarrio, S Guirao-Rico, P Librado, S E Ramos-Onsins, A S\u0026aacute;nchez-Gracia (2017) Dnasp 6: DNA Sequence Polymorphism Analysis of Large Data Sets. \u003cstrong\u003eMolecular biology and evolution\u003c/strong\u003e 34 (12):3299-3302\u003c/li\u003e\n \u003cli\u003eSagart L (2011) How Many Independent Rice Vocabularies in Asia? \u003cstrong\u003eRice\u003c/strong\u003e 4:121-133\u003c/li\u003e\n \u003cli\u003eSagart L, T-F Hsu, Y-C Tsai, C-C Wu, L-T Huang, Y-C Chen, Y-F Chen, Y-C Tseng, H-Y Lin, Y-i C Hsing (2018) A Northern Chinese Origin of Austronesian Agriculture: New Evidence on Traditional Formosan Cereals. \u003cstrong\u003eRice\u003c/strong\u003e 11 (1):1-16\u003c/li\u003e\n \u003cli\u003eSaitoh K, K Onishi, I Mikami, K Thidar, Y Sano (2004) Allelic Diversification at the C (Osc1) Locus of Wild and Cultivated Rice: Nucleotide Changes Associated with Phenotypes. \u003cstrong\u003eGenetics\u003c/strong\u003e 168 (2):997-1007. doi:10.1534/genetics.103.018390\u003c/li\u003e\n \u003cli\u003eSasaki A, M Ashikari, M Ueguchi-Tanaka, H Itoh, A Nishimura, D Swapan, K Ishiyama, T Saito, M Kobayashi, G S Khush (2002) A Mutant Gibberellin-Synthesis Gene in Rice. \u003cstrong\u003eNature\u003c/strong\u003e 416 (6882):701-702\u003c/li\u003e\n \u003cli\u003eShomura A, T Izawa, K Ebana, T Ebitani, H Kanegae, S Konishi, M Yano (2008) Deletion in a Gene Associated with Grain Size Increased Yields During Rice Domestication. \u003cstrong\u003eNat Genet\u003c/strong\u003e 40 (8):1023-1028. doi:10.1038/ng.169\u003c/li\u003e\n \u003cli\u003eSilva F, A Weisskopf, C Castillo, C Murphy, E Kingwell-Banham, L Qin, D Q Fuller (2018) A Tale of Two Rice Varieties: Modelling the Prehistoric Dispersals of Japonica and Proto-Indica Rices. \u003cstrong\u003eThe Holocene\u003c/strong\u003e 28 (11):1745-1758\u003c/li\u003e\n \u003cli\u003eSweeney M T, M J Thomson, B E Pfeil, S McCouch (2006) Caught Red-Handed: Rc Encodes a Basic Helix-Loop-Helix Protein Conditioning Red Pericarp in Rice. \u003cstrong\u003eThe Plant Cell\u003c/strong\u003e 18 (2):283-294. doi:10.1105/tpc.105.038430\u003c/li\u003e\n \u003cli\u003eTajima F (1983) Evolutionary Relationship of DNA Sequences in Finite Populations. \u003cstrong\u003eGenetics\u003c/strong\u003e 105 (2):437-460\u003c/li\u003e\n \u003cli\u003eTajima F (1989) Statistical Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism. \u003cstrong\u003eGenetics\u003c/strong\u003e 123 (3):585-595\u003c/li\u003e\n \u003cli\u003eTakahashi Y, K M Teshima, S Yokoi, H Innan, K Shimamoto (2009) Variations in Hd1 Proteins, Hd3a Promoters, and Ehd1 Expression Levels Contribute to Diversity of Flowering Time in Cultivated Rice. \u003cstrong\u003eProc Natl Acad Sci U S A\u003c/strong\u003e 106 (11):4555-4560. doi:10.1073/pnas.0812092106\u003c/li\u003e\n \u003cli\u003eTamaki S, S Matsuo, H L Wong, S Yokoi, K Shimamoto (2007) Hd3a Protein Is a Mobile Flowering Signal in Rice. \u003cstrong\u003eScience\u003c/strong\u003e 316 (5827):1033-1036\u003c/li\u003e\n \u003cli\u003eTeng Y (2003) Rice Industry Development and Its Future Prospects in Taiwan. \u003cstrong\u003eResearch Bulletin of Kaohsiung District Agricultural Research and Extension Station\u003c/strong\u003e 14:1-23\u003c/li\u003e\n \u003cli\u003eTsang C-H (2005) Recent Discoveries at the Tapenkeng Culture Sites in Taiwan: Implications for the Problem of Austronesian Origins. . \u003cstrong\u003eIn Laurent Sasgart, Roger Blench and Alicia Sanchez-Mazas, eds, The Peopling of East Asia (London: Routledge Curzon)\u003c/strong\u003e:63-74\u003c/li\u003e\n \u003cli\u003eTsang C-H, K-T Li, T-F Hsu, Y-C Tsai, P-H Fang, Y-I C Hsing (2017) Broomcorn and Foxtail Millet Were Cultivated in Taiwan About 5000 Years Ago. \u003cstrong\u003eBotanical studies\u003c/strong\u003e 58 (1):1-10\u003c/li\u003e\n \u003cli\u003eTsuji H, K-i Taoka, K Shimamoto (2013) Florigen in Rice: Complex Gene Network for Florigen Transcription, Florigen Activation Complex, and Multiple Functions. \u003cstrong\u003eCurr Opin Plant Biol\u003c/strong\u003e 16 (2):228-235\u003c/li\u003e\n \u003cli\u003eWang W, R Mauleon, Z Hu, D Chebotarov, S Tai, Z Wu, M Li, T Zheng, R R Fuentes, F Zhang, L Mansueto, D Copetti, M Sanciangco, K C Palis, J Xu, C Sun, B Fu, H Zhang, Y Gao, X Zhao, F Shen, X Cui, H Yu, Z Li, M Chen, J Detras, Y Zhou, X Zhang, Y Zhao, D Kudrna, C Wang, R Li, B Jia, J Lu, X He, Z Dong, J Xu, Y Li, M Wang, J Shi, J Li, D Zhang, S Lee, W Hu, A Poliakov, I Dubchak, V J Ulat, F N Borja, J R Mendoza, J Ali, J Li, Q Gao, Y Niu, Z Yue, M E B Naredo, J Talag, X Wang, J Li, X Fang, Y Yin, J C Glaszmann, J Zhang, J Li, R S Hamilton, R A Wing, J Ruan, G Zhang, C Wei, N Alexandrov, K L McNally, Z Li, H Leung (2018) Genomic Variation in 3,010 Diverse Accessions of Asian Cultivated Rice. \u003cstrong\u003eNature\u003c/strong\u003e 557 (7703):43-49. doi:10.1038/s41586-018-0063-9\u003c/li\u003e\n \u003cli\u003eWang Z Y, F Q Zheng, G Z Shen, J P Gao, D P Snustad, M G Li, J L Zhang, M M Hong (1995) The Amylose Content in Rice Endosperm Is Related to the Post‐Transcriptional Regulation of the Waxy Gene. \u003cstrong\u003eThe Plant Journal\u003c/strong\u003e 7 (4):613-622\u003c/li\u003e\n \u003cli\u003eWatterson G (1975) On the Number of Segregating Sites in Genetical Models without Recombination. \u003cstrong\u003eTheoretical population biology\u003c/strong\u003e 7 (2):256-276\u003c/li\u003e\n \u003cli\u003eWei F-J, Y-C Tsai, Y-M Hsu, Y-A Chen, C-T Huang, H-P Wu, L-T Huang, M-H Lai, L-Y Kuang, S-F Lo (2016a) Lack of Genotype and Phenotype Correlation in a Rice T-DNA Tagged Line Is Likely Caused by Introgression in the Seed Source. \u003cstrong\u003ePLoS One\u003c/strong\u003e 11 (5):e0155768\u003c/li\u003e\n \u003cli\u003eWei F-J, Y-C Tsai, H-P Wu, L-T Huang, Y-C Chen, Y-F Chen, C-C Wu, Y-T Tseng, Y-I C Hsing (2016b) Both Hd1 and Ehd1 Are Important for Artificial Selection of Flowering Time in Cultivated Rice. \u003cstrong\u003ePlant Sci\u003c/strong\u003e 242:187-194\u003c/li\u003e\n \u003cli\u003eWright P (2003) Preservation or Destruction of Plant Remains by Carbonization? \u003cstrong\u003eJ Archaeol Sci\u003c/strong\u003e 30 (5):577-583\u003c/li\u003e\n \u003cli\u003eWu C-C, C-K Liu, F-j Wei, L-T Huang, W-C Lin, Y-T Hsie, M-C Lin, C-H Chan, T-T Le, Y-P Wu, J-C Lo, H-F Li, M-H Lai, S Chen, A-L Hou, W-Y Chiou, S-M Yu, T-H D Ho, Y-I C Hsing (2022) A Rice Genomics and Phenomics Resource with Primarily Taiwan Rice Accessions (A Rice Genomics and Phenomics Resource with Primarily Taiwan Rice Accessions). \u003cstrong\u003eCrop, Environment \u0026amp; Bioinformatics\u003c/strong\u003e 18:12-36. doi:10.30061/ceb.202212_18.0002\u003c/li\u003e\n \u003cli\u003eWu C-C, F-J Wei, W-Y Chiou, Y-C Tsai, H-P Wu, D Gotarkar, Z-H Wei, M-H Lai, Y-I C Hsing (2020a) Studies of Rice Hd1 Haplotypes Worldwide Reveal Adaptation of Flowering Time to Different Environments. \u003cstrong\u003ePLoS One\u003c/strong\u003e 15 (9):e0239028. doi:10.1371/journal.pone.0239028\u003c/li\u003e\n \u003cli\u003eWu D H, D R Gealy, M H Jia, J D Edwards, M H Lai, A M McClung (2020b) Phylogenetic Origin and Dispersal Pattern of Taiwan Weedy Rice. \u003cstrong\u003ePest management science\u003c/strong\u003e 76 (5):1639-1651\u003c/li\u003e\n \u003cli\u003eWu I-L, T Lee, K Li, K-H Lee (2016) The Origin of Rice Cultivation at 4,000 Years Ago on the East Coast of Taiwan: Preliminary Results of Phytolith Analysis. \u003cstrong\u003eJournal of Austronesain Studies\u003c/strong\u003e 6 (1):25-50\u003c/li\u003e\n \u003cli\u003eYano M, Y Katayose, M Ashikari, U Yamanouchi, L Monna, T Fuse, T Baba, K Yamamoto, Y Umehara, Y Nagamura (2000) Hd1, a Major Photoperiod Sensitivity Quantitative Trait Locus in Rice, Is Closely Related to the Arabidopsis Flowering Time Gene Constans. \u003cstrong\u003eThe Plant Cell\u003c/strong\u003e 12 (12):2473-2483\u003c/li\u003e\n \u003cli\u003eYu Y, T Tang, Q Qian, Y Wang, M Yan, D Zeng, B Han, C I Wu, S Shi, J Li (2008) Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication. \u003cstrong\u003ePlant Cell\u003c/strong\u003e 20 (11):2946-2959. doi:10.1105/tpc.108.060426\u003c/li\u003e\n \u003cli\u003eZang Z, K Li (2015) Archaeological Heritage in the Tainan Science Park of Taiwan. National Museum of Prehistory,\u003c/li\u003e\n \u003cli\u003eZhu B F, L Si, Z Wang, Y Zhou, J Zhu, Y Shangguan, D Lu, D Fan, C Li, H Lin, Q Qian, T Sang, B Zhou, Y Minobe, B Han (2011) Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication. \u003cstrong\u003ePlant Physiol\u003c/strong\u003e 155 (3):1301-1311. doi:10.1104/pp.110.168500\u003c/li\u003e\n \u003cli\u003eZhu Z, L Tan, Y Fu, F Liu, H Cai, D Xie, F Wu, J Wu, T Matsumoto, C Sun (2013) Genetic Control of Inflorescence Architecture During Rice Domestication. \u003cstrong\u003eNat Commun\u003c/strong\u003e 4:2200. doi:10.1038/ncomms3200\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Excavated rice grain, genetic diversity, population structure, stress tolerance","lastPublishedDoi":"10.21203/rs.3.rs-3218983/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-3218983/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e \u003cp\u003eCultivation of rice (\u003cem\u003eOryza sativa\u003c/em\u003e) started in Taiwan about 5000 years ago. Here we studied changes in the rice population during this period by using archaeological, morphological, genetic and genomic strategies. We studied the grain size changes of carbonized rice from excavated sites. We also revealed the variations in landraces collected from the indigenous villages and landraces that arrived in Taiwan from southern China about 400 years ago. Some modern varieties were also used in the current study.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e \u003cp\u003eThe very early cultivated rice must have been temperate \u003cem\u003ejaponica\u003c/em\u003e type, and the seeds were relatively small. Rice seeds became relatively bigger around 1500 BP, with some \u003cem\u003eindica\u003c/em\u003e or tropical \u003cem\u003ejaponica\u003c/em\u003e ones. Most, if not all, of the i\u003cem\u003endica\u003c/em\u003e rice were not primitive types, suggesting they arrived in Taiwan rather late. Together, temperate, subtropical, tropical \u003cem\u003ejaponica\u003c/em\u003e and \u003cem\u003eindica\u003c/em\u003e rice have been cultivated by indigenous people for a long period, with all in upland practice. However, only \u003cem\u003eindica\u003c/em\u003e landraces were cultivated in the plain region from the early 17th century to about 100 years ago, when \u003cem\u003ejaponica\u003c/em\u003e rice accessions become dominant. We illustrated huge differences in genetic diversity among the subpopulations of Taiwan rice accessions, and many of these lines showed stress resistance to drought, flooding and ABA treatments.\u003c/p\u003e\u003ch2\u003eConclusion\u003c/h2\u003e \u003cp\u003eWe show how civilization, human migration, taste preference, natural introgression and breeding programs have shaped the population structure of Taiwan rice accessions over thousands of years. We also indicate that Taiwanese indigenous peoples and traditional farmers have kept the rice landraces for hundreds and up to thousands of years. With many old traits preserved, they are good resources for future breeding programs.\u003c/p\u003e","manuscriptTitle":"Population structure dynamics of Taiwan rice accessions over thousands of years as revealed by archaeological, morphological and genome sequencing information","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2023-08-07 12:38:20","doi":"10.21203/rs.3.rs-3218983/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"bbcadfaf-676e-4317-9c7a-c5778ee1b347","owner":[],"postedDate":"August 7th, 2023","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2023-08-22T02:29:12+00:00","versionOfRecord":[],"versionCreatedAt":"2023-08-07 12:38:20","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-3218983","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-3218983","identity":"rs-3218983","version":["v1"]},"buildId":"_2-kVJe1T_tPrBINL-cwx","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}